Multiple sequence alignment - TraesCS7B01G003900

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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 TraesCS7B01G003900 chr7B 100.000 2172 0 0 705 2876 1481986 1484157 0.000000e+00 4012.0
1 TraesCS7B01G003900 chr7B 89.638 1023 87 9 901 1905 1436897 1437918 0.000000e+00 1284.0
2 TraesCS7B01G003900 chr7B 100.000 365 0 0 1 365 1481282 1481646 0.000000e+00 675.0
3 TraesCS7B01G003900 chr7B 90.909 55 4 1 2807 2861 1439478 1439531 3.970000e-09 73.1
4 TraesCS7B01G003900 chr5D 92.404 1514 85 6 901 2393 561573185 561571681 0.000000e+00 2132.0
5 TraesCS7B01G003900 chr5D 89.033 1003 88 12 1021 2001 556273556 556272554 0.000000e+00 1223.0
6 TraesCS7B01G003900 chr5D 87.640 267 14 1 2416 2663 561571508 561571242 2.800000e-75 292.0
7 TraesCS7B01G003900 chr5D 84.656 189 13 10 2690 2876 561570879 561570705 1.060000e-39 174.0
8 TraesCS7B01G003900 chr5D 80.263 228 35 10 1 221 530939270 530939046 2.290000e-36 163.0
9 TraesCS7B01G003900 chr5B 91.905 1396 85 14 999 2393 711268950 711267582 0.000000e+00 1927.0
10 TraesCS7B01G003900 chr5B 90.135 1115 85 16 796 1894 711281153 711280048 0.000000e+00 1426.0
11 TraesCS7B01G003900 chr5B 87.473 455 21 16 2416 2861 711267347 711266920 2.570000e-135 492.0
12 TraesCS7B01G003900 chr5B 85.091 275 18 11 3 273 114912212 114911957 2.840000e-65 259.0
13 TraesCS7B01G003900 chr5B 85.500 200 18 6 2198 2393 711279629 711279437 6.290000e-47 198.0
14 TraesCS7B01G003900 chr5B 79.902 204 17 8 1979 2160 711280036 711279835 8.360000e-26 128.0
15 TraesCS7B01G003900 chr4A 86.627 1660 145 30 795 2393 603665907 603667550 0.000000e+00 1764.0
16 TraesCS7B01G003900 chr4A 78.936 470 42 31 2416 2876 603667733 603668154 1.700000e-67 267.0
17 TraesCS7B01G003900 chr4A 84.962 266 25 8 7 268 116467642 116467896 3.680000e-64 255.0
18 TraesCS7B01G003900 chr4D 88.336 763 87 2 1075 1836 504597468 504598229 0.000000e+00 915.0
19 TraesCS7B01G003900 chr4D 82.857 280 28 12 3 278 483208089 483207826 1.720000e-57 233.0
20 TraesCS7B01G003900 chr4B 87.760 768 92 2 1070 1836 651514487 651515253 0.000000e+00 896.0
21 TraesCS7B01G003900 chr5A 87.811 763 91 2 1075 1836 689251934 689252695 0.000000e+00 893.0
22 TraesCS7B01G003900 chr7D 87.143 280 22 7 3 278 499549359 499549090 3.600000e-79 305.0
23 TraesCS7B01G003900 chr7A 87.313 268 16 8 11 273 565362012 565361758 1.010000e-74 291.0
24 TraesCS7B01G003900 chr2D 89.024 164 14 3 38 198 598302555 598302717 1.750000e-47 200.0
25 TraesCS7B01G003900 chr2D 88.485 165 14 4 38 198 642058150 642058313 8.130000e-46 195.0
26 TraesCS7B01G003900 chr3A 86.207 174 17 7 3 172 86377323 86377493 6.330000e-42 182.0


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 TraesCS7B01G003900 chr7B 1481282 1484157 2875 False 2343.50 4012 100.000000 1 2876 2 chr7B.!!$F2 2875
1 TraesCS7B01G003900 chr7B 1436897 1439531 2634 False 678.55 1284 90.273500 901 2861 2 chr7B.!!$F1 1960
2 TraesCS7B01G003900 chr5D 556272554 556273556 1002 True 1223.00 1223 89.033000 1021 2001 1 chr5D.!!$R2 980
3 TraesCS7B01G003900 chr5D 561570705 561573185 2480 True 866.00 2132 88.233333 901 2876 3 chr5D.!!$R3 1975
4 TraesCS7B01G003900 chr5B 711266920 711268950 2030 True 1209.50 1927 89.689000 999 2861 2 chr5B.!!$R2 1862
5 TraesCS7B01G003900 chr5B 711279437 711281153 1716 True 584.00 1426 85.179000 796 2393 3 chr5B.!!$R3 1597
6 TraesCS7B01G003900 chr4A 603665907 603668154 2247 False 1015.50 1764 82.781500 795 2876 2 chr4A.!!$F2 2081
7 TraesCS7B01G003900 chr4D 504597468 504598229 761 False 915.00 915 88.336000 1075 1836 1 chr4D.!!$F1 761
8 TraesCS7B01G003900 chr4B 651514487 651515253 766 False 896.00 896 87.760000 1070 1836 1 chr4B.!!$F1 766
9 TraesCS7B01G003900 chr5A 689251934 689252695 761 False 893.00 893 87.811000 1075 1836 1 chr5A.!!$F1 761

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
102 103 0.040692 CGCTGCCACATCATACATGC 60.041 55.0 0.0 0.0 0.0 4.06 F
868 875 0.043032 ATGGAAATGGTGGGTGGCAT 59.957 50.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1723 0.331278 TTGCTGGATTGATCCCGGTT 59.669 50.0 0.0 0.0 46.59 4.44 R
2730 3772 0.798776 CGGAACAAAGCACTAGCAGG 59.201 55.0 0.0 0.0 45.49 4.85 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
18 19 3.927555 TTTCTCCCACTAAGCCACG 57.072 52.632 0.00 0.00 0.00 4.94
19 20 0.321298 TTTCTCCCACTAAGCCACGC 60.321 55.000 0.00 0.00 0.00 5.34
20 21 1.476845 TTCTCCCACTAAGCCACGCA 61.477 55.000 0.00 0.00 0.00 5.24
21 22 1.003839 CTCCCACTAAGCCACGCAA 60.004 57.895 0.00 0.00 0.00 4.85
22 23 0.605319 CTCCCACTAAGCCACGCAAA 60.605 55.000 0.00 0.00 0.00 3.68
23 24 0.179015 TCCCACTAAGCCACGCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
24 25 0.887933 CCCACTAAGCCACGCAAAAT 59.112 50.000 0.00 0.00 0.00 1.82
25 26 1.272212 CCCACTAAGCCACGCAAAATT 59.728 47.619 0.00 0.00 0.00 1.82
26 27 2.327568 CCACTAAGCCACGCAAAATTG 58.672 47.619 0.00 0.00 0.00 2.32
40 41 4.566659 CAAAATTGCCACATAAGCGAAC 57.433 40.909 0.00 0.00 0.00 3.95
41 42 4.236935 CAAAATTGCCACATAAGCGAACT 58.763 39.130 0.00 0.00 0.00 3.01
42 43 4.519540 AAATTGCCACATAAGCGAACTT 57.480 36.364 0.00 0.00 40.07 2.66
43 44 5.637006 AAATTGCCACATAAGCGAACTTA 57.363 34.783 0.00 0.00 42.47 2.24
44 45 8.785105 GCAAAATTGCCACATAAGCGAACTTAT 61.785 37.037 6.88 0.00 46.66 1.73
45 46 6.935741 AATTGCCACATAAGCGAACTTATA 57.064 33.333 0.00 0.00 45.41 0.98
46 47 6.935741 ATTGCCACATAAGCGAACTTATAA 57.064 33.333 0.00 0.00 45.41 0.98
47 48 6.745159 TTGCCACATAAGCGAACTTATAAA 57.255 33.333 0.00 0.00 45.41 1.40
48 49 6.935741 TGCCACATAAGCGAACTTATAAAT 57.064 33.333 0.00 0.00 45.41 1.40
49 50 7.328277 TGCCACATAAGCGAACTTATAAATT 57.672 32.000 0.00 0.00 45.41 1.82
50 51 8.439993 TGCCACATAAGCGAACTTATAAATTA 57.560 30.769 0.00 0.00 45.41 1.40
51 52 8.339714 TGCCACATAAGCGAACTTATAAATTAC 58.660 33.333 0.00 0.00 45.41 1.89
52 53 8.339714 GCCACATAAGCGAACTTATAAATTACA 58.660 33.333 0.00 0.00 45.41 2.41
87 88 5.909210 CATTAGTCTATGCATGTAACGCTG 58.091 41.667 10.16 0.00 0.00 5.18
88 89 2.205074 AGTCTATGCATGTAACGCTGC 58.795 47.619 10.16 0.00 38.87 5.25
89 90 1.261619 GTCTATGCATGTAACGCTGCC 59.738 52.381 10.16 0.00 37.59 4.85
90 91 1.134551 TCTATGCATGTAACGCTGCCA 60.135 47.619 10.16 0.00 37.59 4.92
91 92 1.003545 CTATGCATGTAACGCTGCCAC 60.004 52.381 10.16 0.00 37.59 5.01
92 93 0.959867 ATGCATGTAACGCTGCCACA 60.960 50.000 0.00 0.00 37.59 4.17
93 94 0.959867 TGCATGTAACGCTGCCACAT 60.960 50.000 0.00 0.00 37.59 3.21
94 95 0.248215 GCATGTAACGCTGCCACATC 60.248 55.000 6.29 0.83 30.59 3.06
95 96 1.085893 CATGTAACGCTGCCACATCA 58.914 50.000 6.29 0.00 30.59 3.07
96 97 1.672363 CATGTAACGCTGCCACATCAT 59.328 47.619 6.29 0.00 30.59 2.45
97 98 2.682155 TGTAACGCTGCCACATCATA 57.318 45.000 0.00 0.00 0.00 2.15
98 99 2.276201 TGTAACGCTGCCACATCATAC 58.724 47.619 0.00 0.00 0.00 2.39
99 100 2.276201 GTAACGCTGCCACATCATACA 58.724 47.619 0.00 0.00 0.00 2.29
100 101 2.042686 AACGCTGCCACATCATACAT 57.957 45.000 0.00 0.00 0.00 2.29
101 102 1.302366 ACGCTGCCACATCATACATG 58.698 50.000 0.00 0.00 0.00 3.21
102 103 0.040692 CGCTGCCACATCATACATGC 60.041 55.000 0.00 0.00 0.00 4.06
103 104 1.026584 GCTGCCACATCATACATGCA 58.973 50.000 0.00 0.00 0.00 3.96
104 105 1.611977 GCTGCCACATCATACATGCAT 59.388 47.619 0.00 0.00 0.00 3.96
105 106 2.035449 GCTGCCACATCATACATGCATT 59.965 45.455 0.00 0.00 0.00 3.56
106 107 3.253921 GCTGCCACATCATACATGCATTA 59.746 43.478 0.00 0.00 0.00 1.90
107 108 4.615223 GCTGCCACATCATACATGCATTAG 60.615 45.833 0.00 0.00 0.00 1.73
108 109 4.463070 TGCCACATCATACATGCATTAGT 58.537 39.130 0.00 0.00 0.00 2.24
109 110 4.516321 TGCCACATCATACATGCATTAGTC 59.484 41.667 0.00 0.00 0.00 2.59
110 111 4.516321 GCCACATCATACATGCATTAGTCA 59.484 41.667 0.00 0.00 0.00 3.41
111 112 5.182570 GCCACATCATACATGCATTAGTCAT 59.817 40.000 0.00 0.00 0.00 3.06
112 113 6.294342 GCCACATCATACATGCATTAGTCATT 60.294 38.462 0.00 0.00 0.00 2.57
113 114 7.654568 CCACATCATACATGCATTAGTCATTT 58.345 34.615 0.00 0.00 0.00 2.32
114 115 8.139350 CCACATCATACATGCATTAGTCATTTT 58.861 33.333 0.00 0.00 0.00 1.82
115 116 9.524106 CACATCATACATGCATTAGTCATTTTT 57.476 29.630 0.00 0.00 0.00 1.94
116 117 9.740239 ACATCATACATGCATTAGTCATTTTTC 57.260 29.630 0.00 0.00 0.00 2.29
117 118 9.738832 CATCATACATGCATTAGTCATTTTTCA 57.261 29.630 0.00 0.00 0.00 2.69
118 119 9.740239 ATCATACATGCATTAGTCATTTTTCAC 57.260 29.630 0.00 0.00 0.00 3.18
119 120 8.738106 TCATACATGCATTAGTCATTTTTCACA 58.262 29.630 0.00 0.00 0.00 3.58
120 121 9.524106 CATACATGCATTAGTCATTTTTCACAT 57.476 29.630 0.00 0.00 0.00 3.21
122 123 8.836268 ACATGCATTAGTCATTTTTCACATTT 57.164 26.923 0.00 0.00 0.00 2.32
123 124 9.275398 ACATGCATTAGTCATTTTTCACATTTT 57.725 25.926 0.00 0.00 0.00 1.82
124 125 9.749490 CATGCATTAGTCATTTTTCACATTTTC 57.251 29.630 0.00 0.00 0.00 2.29
125 126 9.715121 ATGCATTAGTCATTTTTCACATTTTCT 57.285 25.926 0.00 0.00 0.00 2.52
126 127 9.545105 TGCATTAGTCATTTTTCACATTTTCTT 57.455 25.926 0.00 0.00 0.00 2.52
129 130 8.795786 TTAGTCATTTTTCACATTTTCTTCCG 57.204 30.769 0.00 0.00 0.00 4.30
130 131 7.038154 AGTCATTTTTCACATTTTCTTCCGA 57.962 32.000 0.00 0.00 0.00 4.55
131 132 7.488322 AGTCATTTTTCACATTTTCTTCCGAA 58.512 30.769 0.00 0.00 0.00 4.30
132 133 7.978975 AGTCATTTTTCACATTTTCTTCCGAAA 59.021 29.630 0.00 0.00 37.36 3.46
133 134 8.764287 GTCATTTTTCACATTTTCTTCCGAAAT 58.236 29.630 0.00 0.00 38.81 2.17
134 135 8.763356 TCATTTTTCACATTTTCTTCCGAAATG 58.237 29.630 7.74 7.74 38.81 2.32
135 136 8.763356 CATTTTTCACATTTTCTTCCGAAATGA 58.237 29.630 14.40 1.42 38.81 2.57
136 137 8.885494 TTTTTCACATTTTCTTCCGAAATGAT 57.115 26.923 14.40 0.00 38.81 2.45
137 138 9.973450 TTTTTCACATTTTCTTCCGAAATGATA 57.027 25.926 14.40 2.06 38.81 2.15
147 148 9.562583 TTTCTTCCGAAATGATATTTTTAACGG 57.437 29.630 0.00 0.00 34.35 4.44
148 149 8.271312 TCTTCCGAAATGATATTTTTAACGGT 57.729 30.769 0.00 0.00 39.06 4.83
149 150 9.381033 TCTTCCGAAATGATATTTTTAACGGTA 57.619 29.630 0.00 0.00 39.06 4.02
150 151 9.991388 CTTCCGAAATGATATTTTTAACGGTAA 57.009 29.630 0.00 0.00 39.06 2.85
203 204 9.987272 AGACTTTCTTTTATTGCTTTTATTGCT 57.013 25.926 0.00 0.00 0.00 3.91
260 261 7.299787 AGTTATTTTTAGCAACTACCTACGC 57.700 36.000 0.00 0.00 30.89 4.42
261 262 6.875195 AGTTATTTTTAGCAACTACCTACGCA 59.125 34.615 0.00 0.00 30.89 5.24
262 263 7.551617 AGTTATTTTTAGCAACTACCTACGCAT 59.448 33.333 0.00 0.00 30.89 4.73
263 264 6.753107 ATTTTTAGCAACTACCTACGCATT 57.247 33.333 0.00 0.00 0.00 3.56
264 265 6.563222 TTTTTAGCAACTACCTACGCATTT 57.437 33.333 0.00 0.00 0.00 2.32
265 266 6.563222 TTTTAGCAACTACCTACGCATTTT 57.437 33.333 0.00 0.00 0.00 1.82
266 267 6.563222 TTTAGCAACTACCTACGCATTTTT 57.437 33.333 0.00 0.00 0.00 1.94
296 297 8.438676 AATCTTAATTTCCAAGGACATCTACG 57.561 34.615 0.00 0.00 0.00 3.51
297 298 5.815740 TCTTAATTTCCAAGGACATCTACGC 59.184 40.000 0.00 0.00 0.00 4.42
298 299 3.627395 ATTTCCAAGGACATCTACGCA 57.373 42.857 0.00 0.00 0.00 5.24
299 300 2.672961 TTCCAAGGACATCTACGCAG 57.327 50.000 0.00 0.00 0.00 5.18
301 302 1.476891 TCCAAGGACATCTACGCAGTC 59.523 52.381 0.00 0.00 43.93 3.51
302 303 1.478510 CCAAGGACATCTACGCAGTCT 59.521 52.381 0.00 0.00 43.93 3.24
303 304 2.093973 CCAAGGACATCTACGCAGTCTT 60.094 50.000 0.00 0.00 43.93 3.01
304 305 3.182967 CAAGGACATCTACGCAGTCTTC 58.817 50.000 0.00 0.00 43.93 2.87
305 306 2.447443 AGGACATCTACGCAGTCTTCA 58.553 47.619 0.00 0.00 43.93 3.02
306 307 3.027412 AGGACATCTACGCAGTCTTCAT 58.973 45.455 0.00 0.00 43.93 2.57
307 308 3.067461 AGGACATCTACGCAGTCTTCATC 59.933 47.826 0.00 0.00 43.93 2.92
308 309 3.039405 GACATCTACGCAGTCTTCATCG 58.961 50.000 0.00 0.00 43.93 3.84
309 310 2.223595 ACATCTACGCAGTCTTCATCGG 60.224 50.000 0.00 0.00 43.93 4.18
310 311 1.746470 TCTACGCAGTCTTCATCGGA 58.254 50.000 0.00 0.00 43.93 4.55
311 312 1.671328 TCTACGCAGTCTTCATCGGAG 59.329 52.381 0.00 0.00 43.93 4.63
312 313 1.402259 CTACGCAGTCTTCATCGGAGT 59.598 52.381 0.00 0.00 43.93 3.85
313 314 0.171455 ACGCAGTCTTCATCGGAGTC 59.829 55.000 0.00 0.00 29.74 3.36
314 315 0.171231 CGCAGTCTTCATCGGAGTCA 59.829 55.000 0.00 0.00 0.00 3.41
315 316 1.202348 CGCAGTCTTCATCGGAGTCAT 60.202 52.381 0.00 0.00 0.00 3.06
316 317 2.033424 CGCAGTCTTCATCGGAGTCATA 59.967 50.000 0.00 0.00 0.00 2.15
317 318 3.637432 GCAGTCTTCATCGGAGTCATAG 58.363 50.000 0.00 0.00 0.00 2.23
318 319 3.551863 GCAGTCTTCATCGGAGTCATAGG 60.552 52.174 0.00 0.00 0.00 2.57
319 320 3.634448 CAGTCTTCATCGGAGTCATAGGT 59.366 47.826 0.00 0.00 0.00 3.08
320 321 4.822350 CAGTCTTCATCGGAGTCATAGGTA 59.178 45.833 0.00 0.00 0.00 3.08
321 322 5.049060 CAGTCTTCATCGGAGTCATAGGTAG 60.049 48.000 0.00 0.00 0.00 3.18
322 323 4.822896 GTCTTCATCGGAGTCATAGGTAGT 59.177 45.833 0.00 0.00 0.00 2.73
323 324 5.049267 GTCTTCATCGGAGTCATAGGTAGTC 60.049 48.000 0.00 0.00 0.00 2.59
324 325 4.432980 TCATCGGAGTCATAGGTAGTCA 57.567 45.455 0.00 0.00 0.00 3.41
325 326 4.788679 TCATCGGAGTCATAGGTAGTCAA 58.211 43.478 0.00 0.00 0.00 3.18
326 327 5.198207 TCATCGGAGTCATAGGTAGTCAAA 58.802 41.667 0.00 0.00 0.00 2.69
327 328 5.655090 TCATCGGAGTCATAGGTAGTCAAAA 59.345 40.000 0.00 0.00 0.00 2.44
328 329 5.578005 TCGGAGTCATAGGTAGTCAAAAG 57.422 43.478 0.00 0.00 0.00 2.27
329 330 5.258841 TCGGAGTCATAGGTAGTCAAAAGA 58.741 41.667 0.00 0.00 0.00 2.52
330 331 5.892119 TCGGAGTCATAGGTAGTCAAAAGAT 59.108 40.000 0.00 0.00 0.00 2.40
331 332 6.039493 TCGGAGTCATAGGTAGTCAAAAGATC 59.961 42.308 0.00 0.00 0.00 2.75
332 333 6.183360 CGGAGTCATAGGTAGTCAAAAGATCA 60.183 42.308 0.00 0.00 0.00 2.92
333 334 7.556844 GGAGTCATAGGTAGTCAAAAGATCAA 58.443 38.462 0.00 0.00 0.00 2.57
334 335 8.207545 GGAGTCATAGGTAGTCAAAAGATCAAT 58.792 37.037 0.00 0.00 0.00 2.57
729 730 7.538575 CCTGTATGTTTCAATTTAGGTCTTGG 58.461 38.462 0.00 0.00 0.00 3.61
730 731 7.176690 CCTGTATGTTTCAATTTAGGTCTTGGT 59.823 37.037 0.00 0.00 0.00 3.67
731 732 9.226606 CTGTATGTTTCAATTTAGGTCTTGGTA 57.773 33.333 0.00 0.00 0.00 3.25
732 733 9.575868 TGTATGTTTCAATTTAGGTCTTGGTAA 57.424 29.630 0.00 0.00 0.00 2.85
734 735 8.934023 ATGTTTCAATTTAGGTCTTGGTAAGA 57.066 30.769 0.00 0.00 34.51 2.10
735 736 8.754991 TGTTTCAATTTAGGTCTTGGTAAGAA 57.245 30.769 0.00 0.00 39.67 2.52
736 737 9.191479 TGTTTCAATTTAGGTCTTGGTAAGAAA 57.809 29.630 0.00 0.00 39.67 2.52
769 770 9.905713 ATACAATGTACAAATCTATGTCCACTT 57.094 29.630 0.00 0.00 34.75 3.16
770 771 8.268850 ACAATGTACAAATCTATGTCCACTTC 57.731 34.615 0.00 0.00 34.75 3.01
771 772 8.103305 ACAATGTACAAATCTATGTCCACTTCT 58.897 33.333 0.00 0.00 34.75 2.85
772 773 8.393366 CAATGTACAAATCTATGTCCACTTCTG 58.607 37.037 0.00 0.00 34.75 3.02
773 774 5.874810 TGTACAAATCTATGTCCACTTCTGC 59.125 40.000 0.00 0.00 34.75 4.26
774 775 4.910195 ACAAATCTATGTCCACTTCTGCA 58.090 39.130 0.00 0.00 0.00 4.41
775 776 5.316167 ACAAATCTATGTCCACTTCTGCAA 58.684 37.500 0.00 0.00 0.00 4.08
776 777 5.769662 ACAAATCTATGTCCACTTCTGCAAA 59.230 36.000 0.00 0.00 0.00 3.68
777 778 6.265196 ACAAATCTATGTCCACTTCTGCAAAA 59.735 34.615 0.00 0.00 0.00 2.44
778 779 6.899393 AATCTATGTCCACTTCTGCAAAAA 57.101 33.333 0.00 0.00 0.00 1.94
779 780 5.689383 TCTATGTCCACTTCTGCAAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
780 781 2.842208 TGTCCACTTCTGCAAAAACG 57.158 45.000 0.00 0.00 0.00 3.60
781 782 1.403679 TGTCCACTTCTGCAAAAACGG 59.596 47.619 0.00 0.00 0.00 4.44
782 783 1.404035 GTCCACTTCTGCAAAAACGGT 59.596 47.619 0.00 0.00 0.00 4.83
783 784 1.403679 TCCACTTCTGCAAAAACGGTG 59.596 47.619 0.00 0.00 0.00 4.94
784 785 1.199624 CACTTCTGCAAAAACGGTGC 58.800 50.000 0.00 0.00 42.55 5.01
785 786 0.102300 ACTTCTGCAAAAACGGTGCC 59.898 50.000 0.00 0.00 41.49 5.01
786 787 0.934436 CTTCTGCAAAAACGGTGCCG 60.934 55.000 9.29 9.29 41.49 5.69
787 788 2.945398 TTCTGCAAAAACGGTGCCGC 62.945 55.000 10.87 0.00 44.19 6.53
788 789 4.914420 TGCAAAAACGGTGCCGCG 62.914 61.111 10.87 0.00 44.19 6.46
825 829 8.688151 AGAGAGGTATGACTTGTAAATCAGTAC 58.312 37.037 0.00 0.00 0.00 2.73
830 834 7.769044 GGTATGACTTGTAAATCAGTACATGGT 59.231 37.037 0.00 0.00 34.85 3.55
845 849 3.997762 ACATGGTACTTGTCGCAGTAAA 58.002 40.909 0.00 0.00 30.86 2.01
847 851 4.451096 ACATGGTACTTGTCGCAGTAAAAG 59.549 41.667 0.00 0.00 30.86 2.27
848 852 4.062677 TGGTACTTGTCGCAGTAAAAGT 57.937 40.909 0.00 0.00 36.80 2.66
850 854 5.786311 TGGTACTTGTCGCAGTAAAAGTAT 58.214 37.500 0.00 0.00 37.43 2.12
852 856 5.063060 GGTACTTGTCGCAGTAAAAGTATGG 59.937 44.000 0.00 0.00 37.43 2.74
861 868 5.650543 GCAGTAAAAGTATGGAAATGGTGG 58.349 41.667 0.00 0.00 0.00 4.61
868 875 0.043032 ATGGAAATGGTGGGTGGCAT 59.957 50.000 0.00 0.00 0.00 4.40
895 902 4.946157 GCTAGGGCAAACATATATGCTCAT 59.054 41.667 12.79 0.00 45.61 2.90
896 903 5.416952 GCTAGGGCAAACATATATGCTCATT 59.583 40.000 12.79 0.82 45.61 2.57
898 905 7.121168 GCTAGGGCAAACATATATGCTCATTTA 59.879 37.037 12.79 0.00 45.61 1.40
899 906 7.458409 AGGGCAAACATATATGCTCATTTAG 57.542 36.000 12.79 3.22 45.61 1.85
962 983 3.831323 TGGACATCCATTATTGCCGATT 58.169 40.909 0.00 0.00 42.01 3.34
982 1003 5.106396 CGATTGATCCTTGATTAATCAGCCC 60.106 44.000 17.28 7.96 41.81 5.19
986 1007 4.428294 TCCTTGATTAATCAGCCCAGAG 57.572 45.455 17.28 11.04 38.19 3.35
1023 1054 1.378911 TATGGCAGCAGCACAAGGG 60.379 57.895 2.65 0.00 44.61 3.95
1029 1060 0.321919 CAGCAGCACAAGGGAAGCTA 60.322 55.000 0.00 0.00 36.73 3.32
1347 1378 1.298340 CCACATCAACCCAGCCGTA 59.702 57.895 0.00 0.00 0.00 4.02
1359 1390 2.181525 GCCGTAACGTTCGGGCTA 59.818 61.111 28.14 2.19 46.90 3.93
1530 1561 4.371417 TACTCCAGGACGGCGGGT 62.371 66.667 13.24 0.00 33.14 5.28
1575 1606 2.078914 CGTGCTCGTGTACACCGTC 61.079 63.158 20.11 9.36 33.09 4.79
1581 1612 1.534163 CTCGTGTACACCGTCTTCTCA 59.466 52.381 20.11 0.00 0.00 3.27
1839 1870 4.651503 CACCAGTACATCCTCAGGAATAGT 59.348 45.833 0.00 0.00 34.34 2.12
1867 1898 2.968206 GGTCCAACTACGACGCCT 59.032 61.111 0.00 0.00 0.00 5.52
1881 1920 0.814812 ACGCCTCCGTCTAGCTACTC 60.815 60.000 0.00 0.00 46.39 2.59
1886 1929 2.588620 CTCCGTCTAGCTACTCCCATT 58.411 52.381 0.00 0.00 0.00 3.16
2150 2238 5.789643 TCTCCCTGAATTTTGAAACCTTG 57.210 39.130 0.00 0.00 0.00 3.61
2160 2248 3.799281 TTGAAACCTTGGACTTTGCAG 57.201 42.857 0.00 0.00 0.00 4.41
2175 2422 5.928976 ACTTTGCAGCCCTTTTTATTCTTT 58.071 33.333 0.00 0.00 0.00 2.52
2176 2423 5.759763 ACTTTGCAGCCCTTTTTATTCTTTG 59.240 36.000 0.00 0.00 0.00 2.77
2220 2480 2.413112 CCTAATCAGCAGTGTCACGTTG 59.587 50.000 0.00 1.81 0.00 4.10
2225 2489 1.727022 GCAGTGTCACGTTGCATGC 60.727 57.895 11.82 11.82 37.75 4.06
2316 2580 5.752472 CACTGAATGATTGCTAGTCTACTGG 59.248 44.000 0.00 0.00 0.00 4.00
2318 2582 6.154203 TGAATGATTGCTAGTCTACTGGAG 57.846 41.667 0.00 0.00 0.00 3.86
2319 2583 5.893824 TGAATGATTGCTAGTCTACTGGAGA 59.106 40.000 0.00 0.00 0.00 3.71
2341 2765 7.867403 GGAGACTGCAGTAAAATTCAAATTTGA 59.133 33.333 21.73 16.91 38.53 2.69
2367 2791 5.913137 TGTCCTTTGAGTTTGAACACATT 57.087 34.783 0.00 0.00 29.86 2.71
2525 3196 6.904463 CATGAATGGATGAAATATGGACCA 57.096 37.500 0.00 0.00 0.00 4.02
2591 3291 6.443527 AGGGTTGTCTATATGGCCAAATTTTT 59.556 34.615 10.96 0.00 0.00 1.94
2605 3305 9.347240 TGGCCAAATTTTTAATTGAATCTGAAA 57.653 25.926 0.61 0.00 0.00 2.69
2632 3335 6.489700 TGATGTTTAATGTGTGTCAGACCATT 59.510 34.615 0.00 3.67 33.01 3.16
2634 3337 7.106439 TGTTTAATGTGTGTCAGACCATTTT 57.894 32.000 8.34 3.28 31.66 1.82
2667 3370 6.419771 GCGCCAAATAACTCTGAATTACTAC 58.580 40.000 0.00 0.00 0.00 2.73
2669 3372 7.516943 GCGCCAAATAACTCTGAATTACTACTC 60.517 40.741 0.00 0.00 0.00 2.59
2670 3373 7.042658 CGCCAAATAACTCTGAATTACTACTCC 60.043 40.741 0.00 0.00 0.00 3.85
2671 3374 7.988028 GCCAAATAACTCTGAATTACTACTCCT 59.012 37.037 0.00 0.00 0.00 3.69
2677 3380 8.514330 AACTCTGAATTACTACTCCTACTCTG 57.486 38.462 0.00 0.00 0.00 3.35
2678 3381 7.863722 ACTCTGAATTACTACTCCTACTCTGA 58.136 38.462 0.00 0.00 0.00 3.27
2679 3382 8.330247 ACTCTGAATTACTACTCCTACTCTGAA 58.670 37.037 0.00 0.00 0.00 3.02
2680 3383 9.349713 CTCTGAATTACTACTCCTACTCTGAAT 57.650 37.037 0.00 0.00 0.00 2.57
2730 3772 7.216973 TCTCCTCTTTCACAGTTTACTACTC 57.783 40.000 0.00 0.00 33.85 2.59
2733 3778 6.015350 TCCTCTTTCACAGTTTACTACTCCTG 60.015 42.308 0.00 0.00 33.85 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321298 GCGTGGCTTAGTGGGAGAAA 60.321 55.000 0.00 0.00 0.00 2.52
1 2 1.295423 GCGTGGCTTAGTGGGAGAA 59.705 57.895 0.00 0.00 0.00 2.87
2 3 1.476845 TTGCGTGGCTTAGTGGGAGA 61.477 55.000 0.00 0.00 0.00 3.71
3 4 0.605319 TTTGCGTGGCTTAGTGGGAG 60.605 55.000 0.00 0.00 0.00 4.30
4 5 0.179015 TTTTGCGTGGCTTAGTGGGA 60.179 50.000 0.00 0.00 0.00 4.37
5 6 0.887933 ATTTTGCGTGGCTTAGTGGG 59.112 50.000 0.00 0.00 0.00 4.61
6 7 2.327568 CAATTTTGCGTGGCTTAGTGG 58.672 47.619 0.00 0.00 0.00 4.00
7 8 1.720852 GCAATTTTGCGTGGCTTAGTG 59.279 47.619 0.00 0.00 45.11 2.74
8 9 2.064573 GCAATTTTGCGTGGCTTAGT 57.935 45.000 0.00 0.00 45.11 2.24
18 19 6.806684 AAGTTCGCTTATGTGGCAATTTTGC 61.807 40.000 6.74 6.74 43.68 3.68
19 20 4.236935 AGTTCGCTTATGTGGCAATTTTG 58.763 39.130 0.00 0.00 0.00 2.44
20 21 4.519540 AGTTCGCTTATGTGGCAATTTT 57.480 36.364 0.00 0.00 0.00 1.82
21 22 4.519540 AAGTTCGCTTATGTGGCAATTT 57.480 36.364 0.00 0.00 35.31 1.82
22 23 5.835113 ATAAGTTCGCTTATGTGGCAATT 57.165 34.783 0.00 0.00 45.72 2.32
23 24 6.935741 TTATAAGTTCGCTTATGTGGCAAT 57.064 33.333 9.39 0.00 46.57 3.56
24 25 6.745159 TTTATAAGTTCGCTTATGTGGCAA 57.255 33.333 9.39 0.00 46.57 4.52
25 26 6.935741 ATTTATAAGTTCGCTTATGTGGCA 57.064 33.333 9.39 0.00 46.57 4.92
26 27 8.339714 TGTAATTTATAAGTTCGCTTATGTGGC 58.660 33.333 9.39 0.00 46.57 5.01
50 51 7.707893 GCATAGACTAATGCCAAAAATGATTGT 59.292 33.333 0.00 0.00 45.31 2.71
51 52 8.068893 GCATAGACTAATGCCAAAAATGATTG 57.931 34.615 0.00 0.00 45.31 2.67
64 65 5.613360 GCAGCGTTACATGCATAGACTAATG 60.613 44.000 0.00 0.24 42.11 1.90
65 66 4.449068 GCAGCGTTACATGCATAGACTAAT 59.551 41.667 0.00 0.00 42.11 1.73
66 67 3.802139 GCAGCGTTACATGCATAGACTAA 59.198 43.478 0.00 0.00 42.11 2.24
67 68 3.381045 GCAGCGTTACATGCATAGACTA 58.619 45.455 0.00 0.00 42.11 2.59
68 69 2.205074 GCAGCGTTACATGCATAGACT 58.795 47.619 0.00 0.00 42.11 3.24
69 70 1.261619 GGCAGCGTTACATGCATAGAC 59.738 52.381 0.00 0.00 44.37 2.59
70 71 1.134551 TGGCAGCGTTACATGCATAGA 60.135 47.619 0.00 0.00 44.37 1.98
71 72 1.003545 GTGGCAGCGTTACATGCATAG 60.004 52.381 0.00 0.00 44.37 2.23
72 73 1.013596 GTGGCAGCGTTACATGCATA 58.986 50.000 0.00 0.00 44.37 3.14
73 74 0.959867 TGTGGCAGCGTTACATGCAT 60.960 50.000 10.89 0.00 44.37 3.96
74 75 0.959867 ATGTGGCAGCGTTACATGCA 60.960 50.000 10.89 0.00 44.37 3.96
75 76 0.248215 GATGTGGCAGCGTTACATGC 60.248 55.000 11.85 1.47 41.80 4.06
76 77 1.085893 TGATGTGGCAGCGTTACATG 58.914 50.000 11.85 0.00 35.35 3.21
77 78 2.042686 ATGATGTGGCAGCGTTACAT 57.957 45.000 7.94 7.94 37.72 2.29
78 79 2.276201 GTATGATGTGGCAGCGTTACA 58.724 47.619 0.00 0.00 0.00 2.41
79 80 2.276201 TGTATGATGTGGCAGCGTTAC 58.724 47.619 0.00 0.00 0.00 2.50
80 81 2.682155 TGTATGATGTGGCAGCGTTA 57.318 45.000 0.00 0.00 0.00 3.18
81 82 1.672363 CATGTATGATGTGGCAGCGTT 59.328 47.619 0.00 0.00 0.00 4.84
82 83 1.302366 CATGTATGATGTGGCAGCGT 58.698 50.000 0.00 0.00 0.00 5.07
83 84 0.040692 GCATGTATGATGTGGCAGCG 60.041 55.000 0.00 0.00 0.00 5.18
84 85 1.026584 TGCATGTATGATGTGGCAGC 58.973 50.000 0.00 0.00 0.00 5.25
85 86 4.517832 ACTAATGCATGTATGATGTGGCAG 59.482 41.667 0.00 0.00 34.43 4.85
86 87 4.463070 ACTAATGCATGTATGATGTGGCA 58.537 39.130 0.00 0.00 35.54 4.92
87 88 4.516321 TGACTAATGCATGTATGATGTGGC 59.484 41.667 0.00 0.00 0.00 5.01
88 89 6.812879 ATGACTAATGCATGTATGATGTGG 57.187 37.500 0.00 0.00 0.00 4.17
89 90 9.524106 AAAAATGACTAATGCATGTATGATGTG 57.476 29.630 0.00 0.00 0.00 3.21
90 91 9.740239 GAAAAATGACTAATGCATGTATGATGT 57.260 29.630 0.00 0.00 0.00 3.06
91 92 9.738832 TGAAAAATGACTAATGCATGTATGATG 57.261 29.630 0.00 0.00 0.00 3.07
92 93 9.740239 GTGAAAAATGACTAATGCATGTATGAT 57.260 29.630 0.00 0.00 0.00 2.45
93 94 8.738106 TGTGAAAAATGACTAATGCATGTATGA 58.262 29.630 0.00 0.00 0.00 2.15
94 95 8.914328 TGTGAAAAATGACTAATGCATGTATG 57.086 30.769 0.00 0.00 0.00 2.39
96 97 9.926158 AAATGTGAAAAATGACTAATGCATGTA 57.074 25.926 0.00 0.00 0.00 2.29
97 98 8.836268 AAATGTGAAAAATGACTAATGCATGT 57.164 26.923 0.00 0.00 0.00 3.21
98 99 9.749490 GAAAATGTGAAAAATGACTAATGCATG 57.251 29.630 0.00 0.00 0.00 4.06
99 100 9.715121 AGAAAATGTGAAAAATGACTAATGCAT 57.285 25.926 0.00 0.00 0.00 3.96
100 101 9.545105 AAGAAAATGTGAAAAATGACTAATGCA 57.455 25.926 0.00 0.00 0.00 3.96
103 104 9.410556 CGGAAGAAAATGTGAAAAATGACTAAT 57.589 29.630 0.00 0.00 0.00 1.73
104 105 8.625651 TCGGAAGAAAATGTGAAAAATGACTAA 58.374 29.630 0.00 0.00 37.03 2.24
105 106 8.160521 TCGGAAGAAAATGTGAAAAATGACTA 57.839 30.769 0.00 0.00 37.03 2.59
106 107 7.038154 TCGGAAGAAAATGTGAAAAATGACT 57.962 32.000 0.00 0.00 37.03 3.41
123 124 8.271312 ACCGTTAAAAATATCATTTCGGAAGA 57.729 30.769 15.23 0.00 38.92 2.87
124 125 9.991388 TTACCGTTAAAAATATCATTTCGGAAG 57.009 29.630 15.23 0.00 38.92 3.46
177 178 9.987272 AGCAATAAAAGCAATAAAAGAAAGTCT 57.013 25.926 0.00 0.00 0.00 3.24
234 235 8.872845 GCGTAGGTAGTTGCTAAAAATAACTAA 58.127 33.333 0.00 0.00 38.28 2.24
235 236 8.034215 TGCGTAGGTAGTTGCTAAAAATAACTA 58.966 33.333 0.00 0.00 36.22 2.24
236 237 6.875195 TGCGTAGGTAGTTGCTAAAAATAACT 59.125 34.615 0.00 0.00 38.19 2.24
237 238 7.064060 TGCGTAGGTAGTTGCTAAAAATAAC 57.936 36.000 0.00 0.00 0.00 1.89
238 239 7.852971 ATGCGTAGGTAGTTGCTAAAAATAA 57.147 32.000 0.00 0.00 0.00 1.40
239 240 7.852971 AATGCGTAGGTAGTTGCTAAAAATA 57.147 32.000 0.00 0.00 0.00 1.40
240 241 6.753107 AATGCGTAGGTAGTTGCTAAAAAT 57.247 33.333 0.00 0.00 0.00 1.82
241 242 6.563222 AAATGCGTAGGTAGTTGCTAAAAA 57.437 33.333 0.00 0.00 0.00 1.94
242 243 6.563222 AAAATGCGTAGGTAGTTGCTAAAA 57.437 33.333 0.00 0.00 0.00 1.52
243 244 6.563222 AAAAATGCGTAGGTAGTTGCTAAA 57.437 33.333 0.00 0.00 0.00 1.85
270 271 9.542462 CGTAGATGTCCTTGGAAATTAAGATTA 57.458 33.333 0.00 0.00 0.00 1.75
271 272 7.012421 GCGTAGATGTCCTTGGAAATTAAGATT 59.988 37.037 0.00 0.00 0.00 2.40
272 273 6.483640 GCGTAGATGTCCTTGGAAATTAAGAT 59.516 38.462 0.00 0.00 0.00 2.40
273 274 5.815740 GCGTAGATGTCCTTGGAAATTAAGA 59.184 40.000 0.00 0.00 0.00 2.10
274 275 5.584649 TGCGTAGATGTCCTTGGAAATTAAG 59.415 40.000 0.00 0.00 0.00 1.85
275 276 5.492895 TGCGTAGATGTCCTTGGAAATTAA 58.507 37.500 0.00 0.00 0.00 1.40
276 277 5.092554 TGCGTAGATGTCCTTGGAAATTA 57.907 39.130 0.00 0.00 0.00 1.40
277 278 3.941483 CTGCGTAGATGTCCTTGGAAATT 59.059 43.478 0.00 0.00 0.00 1.82
278 279 3.055094 ACTGCGTAGATGTCCTTGGAAAT 60.055 43.478 7.78 0.00 0.00 2.17
279 280 2.301870 ACTGCGTAGATGTCCTTGGAAA 59.698 45.455 7.78 0.00 0.00 3.13
280 281 1.899814 ACTGCGTAGATGTCCTTGGAA 59.100 47.619 7.78 0.00 0.00 3.53
281 282 1.476891 GACTGCGTAGATGTCCTTGGA 59.523 52.381 7.78 0.00 0.00 3.53
282 283 1.478510 AGACTGCGTAGATGTCCTTGG 59.521 52.381 7.78 0.00 33.20 3.61
283 284 2.949451 AGACTGCGTAGATGTCCTTG 57.051 50.000 7.78 0.00 33.20 3.61
284 285 2.826128 TGAAGACTGCGTAGATGTCCTT 59.174 45.455 7.78 2.43 33.20 3.36
285 286 2.447443 TGAAGACTGCGTAGATGTCCT 58.553 47.619 7.78 0.00 33.20 3.85
286 287 2.941453 TGAAGACTGCGTAGATGTCC 57.059 50.000 7.78 0.00 33.20 4.02
287 288 3.039405 CGATGAAGACTGCGTAGATGTC 58.961 50.000 7.78 1.46 0.00 3.06
288 289 2.223595 CCGATGAAGACTGCGTAGATGT 60.224 50.000 7.78 0.00 0.00 3.06
289 290 2.033424 TCCGATGAAGACTGCGTAGATG 59.967 50.000 7.78 0.00 0.00 2.90
290 291 2.292016 CTCCGATGAAGACTGCGTAGAT 59.708 50.000 7.78 0.00 0.00 1.98
291 292 1.671328 CTCCGATGAAGACTGCGTAGA 59.329 52.381 7.78 0.00 0.00 2.59
292 293 1.402259 ACTCCGATGAAGACTGCGTAG 59.598 52.381 0.00 0.00 0.00 3.51
293 294 1.400846 GACTCCGATGAAGACTGCGTA 59.599 52.381 0.00 0.00 0.00 4.42
294 295 0.171455 GACTCCGATGAAGACTGCGT 59.829 55.000 0.00 0.00 0.00 5.24
295 296 0.171231 TGACTCCGATGAAGACTGCG 59.829 55.000 0.00 0.00 0.00 5.18
296 297 2.593346 ATGACTCCGATGAAGACTGC 57.407 50.000 0.00 0.00 0.00 4.40
297 298 3.634448 ACCTATGACTCCGATGAAGACTG 59.366 47.826 0.00 0.00 0.00 3.51
298 299 3.904717 ACCTATGACTCCGATGAAGACT 58.095 45.455 0.00 0.00 0.00 3.24
299 300 4.822896 ACTACCTATGACTCCGATGAAGAC 59.177 45.833 0.00 0.00 0.00 3.01
300 301 5.050126 ACTACCTATGACTCCGATGAAGA 57.950 43.478 0.00 0.00 0.00 2.87
301 302 4.822350 TGACTACCTATGACTCCGATGAAG 59.178 45.833 0.00 0.00 0.00 3.02
302 303 4.788679 TGACTACCTATGACTCCGATGAA 58.211 43.478 0.00 0.00 0.00 2.57
303 304 4.432980 TGACTACCTATGACTCCGATGA 57.567 45.455 0.00 0.00 0.00 2.92
304 305 5.515797 TTTGACTACCTATGACTCCGATG 57.484 43.478 0.00 0.00 0.00 3.84
305 306 5.892119 TCTTTTGACTACCTATGACTCCGAT 59.108 40.000 0.00 0.00 0.00 4.18
306 307 5.258841 TCTTTTGACTACCTATGACTCCGA 58.741 41.667 0.00 0.00 0.00 4.55
307 308 5.578005 TCTTTTGACTACCTATGACTCCG 57.422 43.478 0.00 0.00 0.00 4.63
308 309 7.113658 TGATCTTTTGACTACCTATGACTCC 57.886 40.000 0.00 0.00 0.00 3.85
704 705 7.176690 ACCAAGACCTAAATTGAAACATACAGG 59.823 37.037 0.00 0.00 0.00 4.00
705 706 8.110860 ACCAAGACCTAAATTGAAACATACAG 57.889 34.615 0.00 0.00 0.00 2.74
706 707 9.575868 TTACCAAGACCTAAATTGAAACATACA 57.424 29.630 0.00 0.00 0.00 2.29
709 710 8.934023 TCTTACCAAGACCTAAATTGAAACAT 57.066 30.769 0.00 0.00 31.20 2.71
710 711 8.754991 TTCTTACCAAGACCTAAATTGAAACA 57.245 30.769 0.00 0.00 37.23 2.83
743 744 9.905713 AAGTGGACATAGATTTGTACATTGTAT 57.094 29.630 0.00 0.00 42.27 2.29
744 745 9.378551 GAAGTGGACATAGATTTGTACATTGTA 57.621 33.333 0.00 0.00 42.27 2.41
745 746 8.103305 AGAAGTGGACATAGATTTGTACATTGT 58.897 33.333 0.00 0.00 42.27 2.71
746 747 8.393366 CAGAAGTGGACATAGATTTGTACATTG 58.607 37.037 0.00 0.00 42.27 2.82
747 748 7.066284 GCAGAAGTGGACATAGATTTGTACATT 59.934 37.037 0.00 0.00 42.27 2.71
748 749 6.540189 GCAGAAGTGGACATAGATTTGTACAT 59.460 38.462 0.00 0.00 42.27 2.29
749 750 5.874810 GCAGAAGTGGACATAGATTTGTACA 59.125 40.000 0.00 0.00 38.13 2.90
750 751 5.874810 TGCAGAAGTGGACATAGATTTGTAC 59.125 40.000 0.00 0.00 0.00 2.90
751 752 6.048732 TGCAGAAGTGGACATAGATTTGTA 57.951 37.500 0.00 0.00 0.00 2.41
752 753 4.910195 TGCAGAAGTGGACATAGATTTGT 58.090 39.130 0.00 0.00 0.00 2.83
753 754 5.885230 TTGCAGAAGTGGACATAGATTTG 57.115 39.130 0.00 0.00 0.00 2.32
754 755 6.899393 TTTTGCAGAAGTGGACATAGATTT 57.101 33.333 0.00 0.00 0.00 2.17
755 756 6.568462 CGTTTTTGCAGAAGTGGACATAGATT 60.568 38.462 0.00 0.00 0.00 2.40
756 757 5.106555 CGTTTTTGCAGAAGTGGACATAGAT 60.107 40.000 0.00 0.00 0.00 1.98
757 758 4.213270 CGTTTTTGCAGAAGTGGACATAGA 59.787 41.667 0.00 0.00 0.00 1.98
758 759 4.466828 CGTTTTTGCAGAAGTGGACATAG 58.533 43.478 0.00 0.00 0.00 2.23
759 760 3.252215 CCGTTTTTGCAGAAGTGGACATA 59.748 43.478 4.16 0.00 0.00 2.29
760 761 2.034558 CCGTTTTTGCAGAAGTGGACAT 59.965 45.455 4.16 0.00 0.00 3.06
761 762 1.403679 CCGTTTTTGCAGAAGTGGACA 59.596 47.619 4.16 0.00 0.00 4.02
762 763 1.404035 ACCGTTTTTGCAGAAGTGGAC 59.596 47.619 14.13 0.00 0.00 4.02
763 764 1.403679 CACCGTTTTTGCAGAAGTGGA 59.596 47.619 14.13 0.00 0.00 4.02
764 765 1.838913 CACCGTTTTTGCAGAAGTGG 58.161 50.000 7.70 7.70 0.00 4.00
765 766 1.199624 GCACCGTTTTTGCAGAAGTG 58.800 50.000 4.13 4.13 39.93 3.16
766 767 0.102300 GGCACCGTTTTTGCAGAAGT 59.898 50.000 0.00 0.00 42.12 3.01
767 768 0.934436 CGGCACCGTTTTTGCAGAAG 60.934 55.000 0.00 0.00 42.12 2.85
768 769 1.064946 CGGCACCGTTTTTGCAGAA 59.935 52.632 0.00 0.00 42.12 3.02
769 770 2.718731 CGGCACCGTTTTTGCAGA 59.281 55.556 0.00 0.00 42.12 4.26
770 771 3.029735 GCGGCACCGTTTTTGCAG 61.030 61.111 11.27 0.00 42.12 4.41
771 772 4.914420 CGCGGCACCGTTTTTGCA 62.914 61.111 11.27 0.00 42.12 4.08
810 811 8.154856 ACAAGTACCATGTACTGATTTACAAGT 58.845 33.333 7.61 0.00 35.60 3.16
825 829 4.451096 ACTTTTACTGCGACAAGTACCATG 59.549 41.667 0.00 0.00 32.39 3.66
830 834 6.028146 TCCATACTTTTACTGCGACAAGTA 57.972 37.500 0.00 0.00 36.43 2.24
845 849 2.888069 GCCACCCACCATTTCCATACTT 60.888 50.000 0.00 0.00 0.00 2.24
847 851 1.111277 GCCACCCACCATTTCCATAC 58.889 55.000 0.00 0.00 0.00 2.39
848 852 0.707024 TGCCACCCACCATTTCCATA 59.293 50.000 0.00 0.00 0.00 2.74
850 854 0.178909 AATGCCACCCACCATTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
852 856 2.483538 GCATAATGCCACCCACCATTTC 60.484 50.000 0.00 0.00 37.42 2.17
861 868 0.178992 TGCCCTAGCATAATGCCACC 60.179 55.000 0.00 0.00 46.52 4.61
881 888 5.416952 GCCAGCCTAAATGAGCATATATGTT 59.583 40.000 14.14 8.22 0.00 2.71
882 889 4.946157 GCCAGCCTAAATGAGCATATATGT 59.054 41.667 14.14 1.43 0.00 2.29
887 894 1.494296 TGGCCAGCCTAAATGAGCATA 59.506 47.619 0.00 0.00 36.94 3.14
895 902 1.212375 TAGAGCATGGCCAGCCTAAA 58.788 50.000 13.05 0.00 36.94 1.85
896 903 1.438469 ATAGAGCATGGCCAGCCTAA 58.562 50.000 13.05 2.13 36.94 2.69
898 905 1.666365 ATATAGAGCATGGCCAGCCT 58.334 50.000 13.05 9.93 36.94 4.58
899 906 3.853355 ATATATAGAGCATGGCCAGCC 57.147 47.619 13.05 4.15 0.00 4.85
952 973 7.665145 TGATTAATCAAGGATCAATCGGCAATA 59.335 33.333 15.82 0.00 33.08 1.90
962 983 4.413189 TCTGGGCTGATTAATCAAGGATCA 59.587 41.667 18.47 11.36 36.18 2.92
982 1003 0.887247 ATGATCGATCTCGGGCTCTG 59.113 55.000 25.02 0.00 40.29 3.35
986 1007 1.739562 GGCATGATCGATCTCGGGC 60.740 63.158 25.02 20.55 40.29 6.13
1023 1054 1.144276 GGCCTCCGGACTTAGCTTC 59.856 63.158 0.00 0.00 0.00 3.86
1029 1060 2.285368 TCCATGGCCTCCGGACTT 60.285 61.111 6.96 0.00 0.00 3.01
1293 1324 1.583495 CGGTGCAGTAGACGAGGACA 61.583 60.000 0.00 0.00 0.00 4.02
1347 1378 1.374252 CAGCAGTAGCCCGAACGTT 60.374 57.895 0.00 0.00 43.56 3.99
1575 1606 2.182030 GGGTCGGTCGCTGAGAAG 59.818 66.667 0.00 0.00 0.00 2.85
1692 1723 0.331278 TTGCTGGATTGATCCCGGTT 59.669 50.000 0.00 0.00 46.59 4.44
1812 1843 3.104512 CCTGAGGATGTACTGGTGGTAA 58.895 50.000 0.00 0.00 31.56 2.85
1839 1870 1.002624 GTTGGACCGGAAGATGGCA 60.003 57.895 9.46 0.00 0.00 4.92
1867 1898 2.092049 TGAATGGGAGTAGCTAGACGGA 60.092 50.000 0.00 0.00 0.00 4.69
1881 1920 4.801330 CATCAATGGATGGATGAATGGG 57.199 45.455 1.66 0.00 45.84 4.00
2150 2238 3.961480 ATAAAAAGGGCTGCAAAGTCC 57.039 42.857 0.50 0.00 0.00 3.85
2160 2248 7.663905 ACCCATAAAACAAAGAATAAAAAGGGC 59.336 33.333 0.00 0.00 32.36 5.19
2175 2422 3.890147 ACGTAGCCAAAACCCATAAAACA 59.110 39.130 0.00 0.00 0.00 2.83
2176 2423 4.508461 ACGTAGCCAAAACCCATAAAAC 57.492 40.909 0.00 0.00 0.00 2.43
2220 2480 5.567552 GTGACATAGAGAAAGAAAGCATGC 58.432 41.667 10.51 10.51 0.00 4.06
2225 2489 4.092091 GTGGCGTGACATAGAGAAAGAAAG 59.908 45.833 0.00 0.00 0.00 2.62
2316 2580 8.694394 GTCAAATTTGAATTTTACTGCAGTCTC 58.306 33.333 25.56 13.36 39.21 3.36
2318 2582 8.579682 AGTCAAATTTGAATTTTACTGCAGTC 57.420 30.769 25.56 8.45 39.84 3.51
2321 2585 9.979578 ACATAGTCAAATTTGAATTTTACTGCA 57.020 25.926 24.43 6.23 40.85 4.41
2341 2765 6.119536 TGTGTTCAAACTCAAAGGACATAGT 58.880 36.000 0.00 0.00 30.36 2.12
2412 2865 9.507280 CGCTGATGAATGAACTAAATTACAAAT 57.493 29.630 0.00 0.00 0.00 2.32
2413 2866 8.511321 ACGCTGATGAATGAACTAAATTACAAA 58.489 29.630 0.00 0.00 0.00 2.83
2448 3117 1.413812 TGTACATGCAGATGCGGATCT 59.586 47.619 14.37 14.37 45.83 2.75
2475 3146 6.422333 TGCATGATTTTTACTCCCTGTATGA 58.578 36.000 0.00 0.00 0.00 2.15
2525 3196 4.320456 CTGCACCCAGCCTCGTGT 62.320 66.667 0.00 0.00 44.83 4.49
2549 3220 3.665675 CTGCGGGTCCAGTGCTACC 62.666 68.421 4.66 4.66 34.85 3.18
2605 3305 6.489700 TGGTCTGACACACATTAAACATCAAT 59.510 34.615 10.38 0.00 0.00 2.57
2632 3335 6.320164 AGAGTTATTTGGCGCCATGTATAAAA 59.680 34.615 33.25 20.31 0.00 1.52
2634 3337 5.238432 CAGAGTTATTTGGCGCCATGTATAA 59.762 40.000 33.25 27.27 0.00 0.98
2667 3370 6.926272 GCACCTGTAATAATTCAGAGTAGGAG 59.074 42.308 0.00 0.00 34.02 3.69
2669 3372 6.582636 TGCACCTGTAATAATTCAGAGTAGG 58.417 40.000 0.00 0.00 34.02 3.18
2670 3373 8.554528 CATTGCACCTGTAATAATTCAGAGTAG 58.445 37.037 0.00 0.00 34.02 2.57
2671 3374 7.012327 GCATTGCACCTGTAATAATTCAGAGTA 59.988 37.037 3.15 0.00 34.02 2.59
2673 3376 6.183360 TGCATTGCACCTGTAATAATTCAGAG 60.183 38.462 7.38 0.00 31.71 3.35
2674 3377 5.651576 TGCATTGCACCTGTAATAATTCAGA 59.348 36.000 7.38 0.00 31.71 3.27
2675 3378 5.893687 TGCATTGCACCTGTAATAATTCAG 58.106 37.500 7.38 0.00 31.71 3.02
2677 3380 7.651808 ACTATGCATTGCACCTGTAATAATTC 58.348 34.615 14.66 0.00 43.04 2.17
2678 3381 7.587037 ACTATGCATTGCACCTGTAATAATT 57.413 32.000 14.66 0.00 43.04 1.40
2679 3382 7.939039 ACTACTATGCATTGCACCTGTAATAAT 59.061 33.333 14.66 0.00 43.04 1.28
2680 3383 7.279615 ACTACTATGCATTGCACCTGTAATAA 58.720 34.615 14.66 0.00 43.04 1.40
2682 3385 5.684704 ACTACTATGCATTGCACCTGTAAT 58.315 37.500 14.66 4.75 43.04 1.89
2685 3388 3.634397 ACTACTATGCATTGCACCTGT 57.366 42.857 14.66 14.52 43.04 4.00
2688 3391 3.561725 GGAGAACTACTATGCATTGCACC 59.438 47.826 14.66 2.61 43.04 5.01
2730 3772 0.798776 CGGAACAAAGCACTAGCAGG 59.201 55.000 0.00 0.00 45.49 4.85
2733 3778 1.132640 CGCGGAACAAAGCACTAGC 59.867 57.895 0.00 0.00 42.56 3.42


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

AutoCloner maintained by Alex Coulton.