Multiple sequence alignment - TraesCS7D01G444100

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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 TraesCS7D01G444100 chr7D 100.000 7723 0 0 1 7723 564966699 564974421 0.000000e+00 14262.0
1 TraesCS7D01G444100 chr7D 88.750 400 30 9 6652 7045 565016428 565016818 7.010000e-130 475.0
2 TraesCS7D01G444100 chr7D 91.096 146 13 0 7578 7723 565042292 565042437 1.700000e-46 198.0
3 TraesCS7D01G444100 chr7D 78.313 332 47 18 7181 7506 565164976 565165288 2.840000e-44 191.0
4 TraesCS7D01G444100 chr7D 87.162 148 19 0 5806 5953 565069476 565069623 1.330000e-37 169.0
5 TraesCS7D01G444100 chr7D 78.000 300 43 17 7157 7452 565016671 565016951 4.790000e-37 167.0
6 TraesCS7D01G444100 chr7D 84.211 152 18 5 7157 7305 564973595 564973743 8.080000e-30 143.0
7 TraesCS7D01G444100 chr7D 84.314 153 16 7 6897 7045 564973855 564974003 8.080000e-30 143.0
8 TraesCS7D01G444100 chr7D 90.000 60 6 0 7057 7116 565016852 565016911 2.310000e-10 78.7
9 TraesCS7D01G444100 chr7A 93.221 6874 276 77 3 6757 650621399 650628201 0.000000e+00 9937.0
10 TraesCS7D01G444100 chr7A 94.957 932 32 7 5974 6902 650720254 650721173 0.000000e+00 1447.0
11 TraesCS7D01G444100 chr7A 86.667 1155 105 23 5799 6922 650891117 650892253 0.000000e+00 1234.0
12 TraesCS7D01G444100 chr7A 86.667 1155 105 23 5799 6922 650904294 650905430 0.000000e+00 1234.0
13 TraesCS7D01G444100 chr7A 89.744 429 41 3 5548 5975 650675032 650675458 5.270000e-151 545.0
14 TraesCS7D01G444100 chr7A 85.498 462 53 9 5989 6437 650865658 650866118 3.260000e-128 470.0
15 TraesCS7D01G444100 chr7A 82.561 453 57 15 5069 5503 650688857 650689305 5.660000e-101 379.0
16 TraesCS7D01G444100 chr7A 82.159 454 58 15 5069 5503 650674592 650675041 1.220000e-97 368.0
17 TraesCS7D01G444100 chr7A 93.450 229 15 0 6895 7123 650773524 650773752 2.670000e-89 340.0
18 TraesCS7D01G444100 chr7A 81.573 445 52 16 5069 5501 650816190 650816616 2.670000e-89 340.0
19 TraesCS7D01G444100 chr7A 91.165 249 21 1 4790 5037 650815946 650816194 3.450000e-88 337.0
20 TraesCS7D01G444100 chr7A 90.361 249 23 1 4790 5037 650674348 650674596 7.470000e-85 326.0
21 TraesCS7D01G444100 chr7A 89.919 248 24 1 4791 5037 650688614 650688861 1.250000e-82 318.0
22 TraesCS7D01G444100 chr7A 89.451 237 23 2 5548 5783 650816609 650816844 1.630000e-76 298.0
23 TraesCS7D01G444100 chr7A 88.500 200 18 3 6847 7045 650629906 650630101 3.600000e-58 237.0
24 TraesCS7D01G444100 chr7A 73.782 595 85 42 7157 7723 650629957 650630508 1.330000e-37 169.0
25 TraesCS7D01G444100 chr7A 85.827 127 15 2 7181 7305 650892450 650892575 1.750000e-26 132.0
26 TraesCS7D01G444100 chr7A 85.827 127 15 2 7181 7305 650905627 650905752 1.750000e-26 132.0
27 TraesCS7D01G444100 chr7A 94.937 79 4 0 5897 5975 650819653 650819731 2.930000e-24 124.0
28 TraesCS7D01G444100 chr7A 80.240 167 21 8 6641 6801 650815744 650815904 1.760000e-21 115.0
29 TraesCS7D01G444100 chr7A 90.588 85 8 0 5819 5903 650816842 650816926 6.330000e-21 113.0
30 TraesCS7D01G444100 chr7B 96.640 3988 88 16 3143 7123 614870604 614874552 0.000000e+00 6580.0
31 TraesCS7D01G444100 chr7B 95.005 1061 37 4 1964 3012 614869553 614870609 0.000000e+00 1652.0
32 TraesCS7D01G444100 chr7B 86.913 1406 95 42 453 1821 614867911 614869264 0.000000e+00 1495.0
33 TraesCS7D01G444100 chr7B 95.455 902 32 4 5564 6463 614914038 614914932 0.000000e+00 1430.0
34 TraesCS7D01G444100 chr7B 92.491 546 30 4 6461 7002 614915360 614915898 0.000000e+00 771.0
35 TraesCS7D01G444100 chr7B 91.205 523 44 2 7203 7723 614918260 614918782 0.000000e+00 710.0
36 TraesCS7D01G444100 chr7B 93.059 389 19 3 7189 7569 614876820 614877208 5.230000e-156 562.0
37 TraesCS7D01G444100 chr7B 91.005 378 31 3 4790 5166 614907870 614908245 2.490000e-139 507.0
38 TraesCS7D01G444100 chr7B 89.865 148 9 2 6539 6683 614903027 614903171 1.320000e-42 185.0
39 TraesCS7D01G444100 chr7B 77.852 298 41 21 7193 7484 615242616 615242894 2.230000e-35 161.0
40 TraesCS7D01G444100 chr7B 92.593 108 8 0 6931 7038 615242615 615242722 1.040000e-33 156.0
41 TraesCS7D01G444100 chr7B 94.382 89 4 1 7035 7123 614917251 614917338 1.350000e-27 135.0
42 TraesCS7D01G444100 chr7B 85.714 119 12 4 6929 7045 614876821 614876936 3.790000e-23 121.0
43 TraesCS7D01G444100 chr1D 76.456 1185 233 34 5325 6479 465534707 465535875 1.110000e-167 601.0
44 TraesCS7D01G444100 chr1D 85.027 187 26 2 1264 1449 465531315 465531500 1.020000e-43 189.0
45 TraesCS7D01G444100 chr1A 75.820 1158 227 39 5358 6479 557951251 557952391 8.820000e-149 538.0
46 TraesCS7D01G444100 chr1A 85.052 194 21 6 1264 1453 557948096 557948285 2.840000e-44 191.0
47 TraesCS7D01G444100 chr4A 82.437 279 36 2 3533 3811 31395398 31395663 1.680000e-56 231.0
48 TraesCS7D01G444100 chr1B 86.082 194 19 6 1264 1453 642470823 642471012 1.310000e-47 202.0


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 TraesCS7D01G444100 chr7D 564966699 564974421 7722 False 4849.333333 14262 89.508333 1 7723 3 chr7D.!!$F4 7722
1 TraesCS7D01G444100 chr7D 565016428 565016951 523 False 240.233333 475 85.583333 6652 7452 3 chr7D.!!$F5 800
2 TraesCS7D01G444100 chr7A 650621399 650630508 9109 False 3447.666667 9937 85.167667 3 7723 3 chr7A.!!$F4 7720
3 TraesCS7D01G444100 chr7A 650720254 650721173 919 False 1447.000000 1447 94.957000 5974 6902 1 chr7A.!!$F1 928
4 TraesCS7D01G444100 chr7A 650891117 650892575 1458 False 683.000000 1234 86.247000 5799 7305 2 chr7A.!!$F8 1506
5 TraesCS7D01G444100 chr7A 650904294 650905752 1458 False 683.000000 1234 86.247000 5799 7305 2 chr7A.!!$F9 1506
6 TraesCS7D01G444100 chr7A 650674348 650675458 1110 False 413.000000 545 87.421333 4790 5975 3 chr7A.!!$F5 1185
7 TraesCS7D01G444100 chr7A 650688614 650689305 691 False 348.500000 379 86.240000 4791 5503 2 chr7A.!!$F6 712
8 TraesCS7D01G444100 chr7A 650815744 650819731 3987 False 221.166667 340 87.992333 4790 6801 6 chr7A.!!$F7 2011
9 TraesCS7D01G444100 chr7B 614867911 614877208 9297 False 2082.000000 6580 91.466200 453 7569 5 chr7B.!!$F3 7116
10 TraesCS7D01G444100 chr7B 614914038 614918782 4744 False 761.500000 1430 93.383250 5564 7723 4 chr7B.!!$F4 2159
11 TraesCS7D01G444100 chr1D 465531315 465535875 4560 False 395.000000 601 80.741500 1264 6479 2 chr1D.!!$F1 5215
12 TraesCS7D01G444100 chr1A 557948096 557952391 4295 False 364.500000 538 80.436000 1264 6479 2 chr1A.!!$F1 5215

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
820 874 0.038067 ACGCACCATACAACACGCTA 60.038 50.000 0.00 0.0 0.00 4.26 F
968 1039 0.174617 CCAGCTCGTCCTCTTCTTCC 59.825 60.000 0.00 0.0 0.00 3.46 F
969 1040 0.174617 CAGCTCGTCCTCTTCTTCCC 59.825 60.000 0.00 0.0 0.00 3.97 F
2122 2405 0.179065 TGCATCTCAATCTGCTCCCG 60.179 55.000 0.00 0.0 39.16 5.14 F
3064 3641 1.405105 CATTAAACCCATGGACCTGCG 59.595 52.381 15.22 0.0 0.00 5.18 F
3814 4399 1.089920 CAGCCATTCCTCCAAACTCG 58.910 55.000 0.00 0.0 0.00 4.18 F
4513 5098 0.808847 GGAAGCCACCGAATACGTCC 60.809 60.000 0.00 0.0 37.88 4.79 F
6173 9566 2.753029 GGAGCAGTCAGGCTTGGT 59.247 61.111 0.00 0.0 45.99 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2619 1.412710 TCAGACAGAAAGACAACGGCT 59.587 47.619 0.00 0.0 0.00 5.52 R
2606 3137 3.788227 AGCACAGTTGGTTTCTCCATA 57.212 42.857 0.00 0.0 46.60 2.74 R
2968 3545 7.119846 AGCCTTCTAAATTTGTGCTAGTACTTG 59.880 37.037 12.42 0.0 0.00 3.16 R
3104 3681 1.681229 AAAAGGGAGGTGGCTATCCA 58.319 50.000 5.74 0.0 40.85 3.41 R
4513 5098 0.528249 GCAACTGTTGGGCACTTGTG 60.528 55.000 21.01 0.0 0.00 3.33 R
4981 5577 1.795768 CTTTTCTCACTGGCGCTACA 58.204 50.000 7.64 0.0 0.00 2.74 R
6324 9735 1.636148 ATTTGAGCAATGGTGGCAGT 58.364 45.000 0.00 0.0 0.00 4.40 R
7211 16462 0.597637 GGATGATACTGTCCGCACCG 60.598 60.000 0.00 0.0 0.00 4.94 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
30 31 1.750778 CCATCGCCACCTAAGCAAATT 59.249 47.619 0.00 0.00 0.00 1.82
34 35 1.133025 CGCCACCTAAGCAAATTGAGG 59.867 52.381 0.00 0.00 35.05 3.86
35 36 1.134995 GCCACCTAAGCAAATTGAGGC 60.135 52.381 0.00 0.00 31.81 4.70
38 39 0.101219 CCTAAGCAAATTGAGGCCGC 59.899 55.000 0.00 0.00 0.00 6.53
52 53 3.056313 GCCGCAGCCAAATCTCCAC 62.056 63.158 0.00 0.00 0.00 4.02
66 67 1.270826 TCTCCACTCAGAGCTTTGACG 59.729 52.381 2.15 2.85 33.66 4.35
74 75 4.504132 AGCTTTGACGCTCCGATC 57.496 55.556 0.00 0.00 34.57 3.69
86 87 5.938710 TGACGCTCCGATCTAGACTTATTAT 59.061 40.000 0.00 0.00 0.00 1.28
90 91 6.557110 GCTCCGATCTAGACTTATTATCACC 58.443 44.000 0.00 0.00 0.00 4.02
95 97 9.621629 CCGATCTAGACTTATTATCACCTCTAT 57.378 37.037 0.00 0.00 0.00 1.98
102 104 9.084533 AGACTTATTATCACCTCTATCCAAGTC 57.915 37.037 0.00 0.00 38.80 3.01
103 105 8.783660 ACTTATTATCACCTCTATCCAAGTCA 57.216 34.615 0.00 0.00 0.00 3.41
109 111 4.162320 TCACCTCTATCCAAGTCAATGGTC 59.838 45.833 0.00 0.00 41.46 4.02
116 118 4.387026 TCCAAGTCAATGGTCCAGAAAT 57.613 40.909 0.00 0.00 41.46 2.17
120 123 5.587844 CCAAGTCAATGGTCCAGAAATAGAG 59.412 44.000 0.00 0.00 35.65 2.43
121 124 5.365021 AGTCAATGGTCCAGAAATAGAGG 57.635 43.478 0.00 0.00 0.00 3.69
126 129 2.852449 TGGTCCAGAAATAGAGGCCAAT 59.148 45.455 5.01 0.00 0.00 3.16
128 131 4.141482 TGGTCCAGAAATAGAGGCCAATAC 60.141 45.833 5.01 0.00 0.00 1.89
141 144 3.008375 AGGCCAATACATAGATCACGCAT 59.992 43.478 5.01 0.00 0.00 4.73
144 147 4.452114 GCCAATACATAGATCACGCATCAA 59.548 41.667 0.00 0.00 33.29 2.57
145 148 5.615544 GCCAATACATAGATCACGCATCAAC 60.616 44.000 0.00 0.00 33.29 3.18
146 149 5.466393 CCAATACATAGATCACGCATCAACA 59.534 40.000 0.00 0.00 33.29 3.33
147 150 6.148315 CCAATACATAGATCACGCATCAACAT 59.852 38.462 0.00 0.00 33.29 2.71
149 152 8.378421 CAATACATAGATCACGCATCAACATAG 58.622 37.037 0.00 0.00 33.29 2.23
151 154 6.515832 ACATAGATCACGCATCAACATAGAA 58.484 36.000 0.00 0.00 33.29 2.10
153 156 4.122776 AGATCACGCATCAACATAGAACC 58.877 43.478 0.00 0.00 33.29 3.62
157 160 3.062639 CACGCATCAACATAGAACCTCAC 59.937 47.826 0.00 0.00 0.00 3.51
158 161 3.261580 CGCATCAACATAGAACCTCACA 58.738 45.455 0.00 0.00 0.00 3.58
161 164 5.575957 GCATCAACATAGAACCTCACATTG 58.424 41.667 0.00 0.00 0.00 2.82
163 166 6.549061 CATCAACATAGAACCTCACATTGTG 58.451 40.000 10.64 10.64 34.45 3.33
164 167 5.620206 TCAACATAGAACCTCACATTGTGT 58.380 37.500 16.06 0.00 34.79 3.72
165 168 6.061441 TCAACATAGAACCTCACATTGTGTT 58.939 36.000 16.06 3.91 34.79 3.32
167 170 4.690748 ACATAGAACCTCACATTGTGTTCG 59.309 41.667 16.06 7.62 41.43 3.95
168 171 3.469008 AGAACCTCACATTGTGTTCGA 57.531 42.857 16.06 0.00 41.43 3.71
169 172 3.131396 AGAACCTCACATTGTGTTCGAC 58.869 45.455 16.06 7.17 41.43 4.20
170 173 1.497991 ACCTCACATTGTGTTCGACG 58.502 50.000 16.06 0.00 34.79 5.12
171 174 1.202486 ACCTCACATTGTGTTCGACGT 60.202 47.619 16.06 0.00 34.79 4.34
172 175 1.864711 CCTCACATTGTGTTCGACGTT 59.135 47.619 16.06 0.00 34.79 3.99
177 180 3.244345 CACATTGTGTTCGACGTTAGTGT 59.756 43.478 8.69 0.00 0.00 3.55
178 181 3.244345 ACATTGTGTTCGACGTTAGTGTG 59.756 43.478 0.00 0.00 0.00 3.82
179 182 1.842720 TGTGTTCGACGTTAGTGTGG 58.157 50.000 0.00 0.00 0.00 4.17
180 183 1.134753 TGTGTTCGACGTTAGTGTGGT 59.865 47.619 0.00 0.00 0.00 4.16
181 184 2.195922 GTGTTCGACGTTAGTGTGGTT 58.804 47.619 0.00 0.00 0.00 3.67
186 189 3.371168 TCGACGTTAGTGTGGTTACAAC 58.629 45.455 0.00 0.00 38.82 3.32
187 190 3.114809 CGACGTTAGTGTGGTTACAACA 58.885 45.455 0.00 0.00 38.82 3.33
188 191 3.180980 CGACGTTAGTGTGGTTACAACAG 59.819 47.826 0.00 0.00 38.82 3.16
190 193 4.952460 ACGTTAGTGTGGTTACAACAGAT 58.048 39.130 0.00 0.00 38.82 2.90
194 197 6.129009 CGTTAGTGTGGTTACAACAGATGTAC 60.129 42.308 0.00 0.00 44.11 2.90
203 209 6.915843 GGTTACAACAGATGTACACAAAAAGG 59.084 38.462 0.00 0.00 44.11 3.11
206 212 9.562408 TTACAACAGATGTACACAAAAAGGATA 57.438 29.630 0.00 0.00 44.11 2.59
239 245 1.002251 CGCTTCTACCATCTCGGAGTC 60.002 57.143 4.69 0.00 38.63 3.36
242 248 2.932855 TCTACCATCTCGGAGTCGAT 57.067 50.000 4.69 0.00 45.04 3.59
246 252 1.883275 ACCATCTCGGAGTCGATGATC 59.117 52.381 4.69 0.00 45.04 2.92
267 273 1.453155 GACAATCGTGCCATCCACTT 58.547 50.000 0.00 0.00 42.42 3.16
272 278 0.107643 TCGTGCCATCCACTTCACAA 59.892 50.000 0.00 0.00 42.42 3.33
276 282 0.238289 GCCATCCACTTCACAACACG 59.762 55.000 0.00 0.00 0.00 4.49
280 289 1.885388 CCACTTCACAACACGCCGA 60.885 57.895 0.00 0.00 0.00 5.54
288 297 2.050351 AACACGCCGACGAGACTG 60.050 61.111 0.00 0.00 43.93 3.51
300 309 2.361357 AGACTGCCGCCTACGAGT 60.361 61.111 0.00 0.00 43.93 4.18
302 311 3.701604 GACTGCCGCCTACGAGTGG 62.702 68.421 0.00 0.00 43.93 4.00
310 319 1.742768 CCTACGAGTGGCATCCCTC 59.257 63.158 0.00 0.00 0.00 4.30
334 343 2.290323 GCGGCCTACCAATCTCCATAAT 60.290 50.000 0.00 0.00 34.57 1.28
336 345 3.084786 GGCCTACCAATCTCCATAATGC 58.915 50.000 0.00 0.00 35.26 3.56
339 348 4.248859 CCTACCAATCTCCATAATGCTCG 58.751 47.826 0.00 0.00 0.00 5.03
342 351 2.497138 CAATCTCCATAATGCTCGCCA 58.503 47.619 0.00 0.00 0.00 5.69
369 378 4.333095 CGGAGTGCATCGGATCTG 57.667 61.111 0.00 0.00 0.00 2.90
377 386 1.072678 CATCGGATCTGGGCAGCAT 59.927 57.895 0.62 0.00 0.00 3.79
378 387 1.072678 ATCGGATCTGGGCAGCATG 59.927 57.895 0.62 0.00 40.87 4.06
396 405 2.112815 GGGTGCCAAGTATGTCGCC 61.113 63.158 0.00 0.00 0.00 5.54
433 444 4.351503 CGACGACGCTCTTCTCTG 57.648 61.111 0.00 0.00 0.00 3.35
435 446 1.515304 GACGACGCTCTTCTCTGCC 60.515 63.158 0.00 0.00 0.00 4.85
436 447 2.578178 CGACGCTCTTCTCTGCCG 60.578 66.667 0.00 0.00 0.00 5.69
438 449 3.633094 GACGCTCTTCTCTGCCGCA 62.633 63.158 0.00 0.00 0.00 5.69
440 451 2.817396 GCTCTTCTCTGCCGCACC 60.817 66.667 0.00 0.00 0.00 5.01
441 452 2.125350 CTCTTCTCTGCCGCACCC 60.125 66.667 0.00 0.00 0.00 4.61
442 453 2.604686 TCTTCTCTGCCGCACCCT 60.605 61.111 0.00 0.00 0.00 4.34
443 454 2.435586 CTTCTCTGCCGCACCCTG 60.436 66.667 0.00 0.00 0.00 4.45
444 455 2.922503 TTCTCTGCCGCACCCTGA 60.923 61.111 0.00 0.00 0.00 3.86
445 456 2.249413 CTTCTCTGCCGCACCCTGAT 62.249 60.000 0.00 0.00 0.00 2.90
446 457 0.975556 TTCTCTGCCGCACCCTGATA 60.976 55.000 0.00 0.00 0.00 2.15
447 458 0.975556 TCTCTGCCGCACCCTGATAA 60.976 55.000 0.00 0.00 0.00 1.75
448 459 0.811616 CTCTGCCGCACCCTGATAAC 60.812 60.000 0.00 0.00 0.00 1.89
450 461 0.676466 CTGCCGCACCCTGATAACAA 60.676 55.000 0.00 0.00 0.00 2.83
451 462 0.676466 TGCCGCACCCTGATAACAAG 60.676 55.000 0.00 0.00 0.00 3.16
454 467 0.739462 CGCACCCTGATAACAAGCGA 60.739 55.000 0.00 0.00 45.78 4.93
512 526 6.738114 ACAAATTCAACCACATGAACACTAG 58.262 36.000 0.00 0.00 41.78 2.57
518 532 6.530120 TCAACCACATGAACACTAGTACAAT 58.470 36.000 0.00 0.00 0.00 2.71
707 747 2.014068 GCCATCCAACAGTAGCTGTCC 61.014 57.143 0.00 0.00 44.62 4.02
768 813 3.772560 CACACACGCGCGCATACA 61.773 61.111 32.58 0.00 0.00 2.29
769 814 3.773630 ACACACGCGCGCATACAC 61.774 61.111 32.58 0.00 0.00 2.90
770 815 4.826605 CACACGCGCGCATACACG 62.827 66.667 32.58 16.12 0.00 4.49
812 866 2.740440 CGCACCACGCACCATACA 60.740 61.111 0.00 0.00 42.60 2.29
813 867 2.321333 CGCACCACGCACCATACAA 61.321 57.895 0.00 0.00 42.60 2.41
814 868 1.209127 GCACCACGCACCATACAAC 59.791 57.895 0.00 0.00 41.79 3.32
815 869 1.511318 GCACCACGCACCATACAACA 61.511 55.000 0.00 0.00 41.79 3.33
817 871 1.225376 ACCACGCACCATACAACACG 61.225 55.000 0.00 0.00 0.00 4.49
818 872 1.154488 CACGCACCATACAACACGC 60.154 57.895 0.00 0.00 0.00 5.34
819 873 1.301401 ACGCACCATACAACACGCT 60.301 52.632 0.00 0.00 0.00 5.07
820 874 0.038067 ACGCACCATACAACACGCTA 60.038 50.000 0.00 0.00 0.00 4.26
821 875 0.368907 CGCACCATACAACACGCTAC 59.631 55.000 0.00 0.00 0.00 3.58
822 876 1.434555 GCACCATACAACACGCTACA 58.565 50.000 0.00 0.00 0.00 2.74
823 877 2.006888 GCACCATACAACACGCTACAT 58.993 47.619 0.00 0.00 0.00 2.29
824 878 2.030457 GCACCATACAACACGCTACATC 59.970 50.000 0.00 0.00 0.00 3.06
825 879 2.607635 CACCATACAACACGCTACATCC 59.392 50.000 0.00 0.00 0.00 3.51
826 880 2.210116 CCATACAACACGCTACATCCC 58.790 52.381 0.00 0.00 0.00 3.85
827 881 2.158957 CCATACAACACGCTACATCCCT 60.159 50.000 0.00 0.00 0.00 4.20
828 882 2.665649 TACAACACGCTACATCCCTG 57.334 50.000 0.00 0.00 0.00 4.45
829 883 0.673644 ACAACACGCTACATCCCTGC 60.674 55.000 0.00 0.00 0.00 4.85
834 888 4.530857 GCTACATCCCTGCGCCGT 62.531 66.667 4.18 0.00 0.00 5.68
835 889 2.186903 CTACATCCCTGCGCCGTT 59.813 61.111 4.18 0.00 0.00 4.44
836 890 2.125310 TACATCCCTGCGCCGTTG 60.125 61.111 4.18 0.14 0.00 4.10
837 891 2.852495 CTACATCCCTGCGCCGTTGT 62.852 60.000 4.18 6.56 0.00 3.32
838 892 2.845752 TACATCCCTGCGCCGTTGTC 62.846 60.000 4.18 0.00 0.00 3.18
839 893 4.015406 ATCCCTGCGCCGTTGTCA 62.015 61.111 4.18 0.00 0.00 3.58
840 894 3.958147 ATCCCTGCGCCGTTGTCAG 62.958 63.158 4.18 0.00 0.00 3.51
841 895 4.988598 CCCTGCGCCGTTGTCAGT 62.989 66.667 4.18 0.00 0.00 3.41
861 916 1.550130 CCCGTTGGACTCCCTGCTAA 61.550 60.000 0.00 0.00 0.00 3.09
897 956 0.667487 CGCCGTCAAGCTCTCTTTCA 60.667 55.000 0.00 0.00 0.00 2.69
927 992 3.847602 CAGGGCGGAGGAGCAGAG 61.848 72.222 0.00 0.00 39.27 3.35
968 1039 0.174617 CCAGCTCGTCCTCTTCTTCC 59.825 60.000 0.00 0.00 0.00 3.46
969 1040 0.174617 CAGCTCGTCCTCTTCTTCCC 59.825 60.000 0.00 0.00 0.00 3.97
971 1042 1.258445 GCTCGTCCTCTTCTTCCCCA 61.258 60.000 0.00 0.00 0.00 4.96
972 1043 0.533032 CTCGTCCTCTTCTTCCCCAC 59.467 60.000 0.00 0.00 0.00 4.61
976 1047 1.229984 CCTCTTCTTCCCCACCCCT 60.230 63.158 0.00 0.00 0.00 4.79
978 1049 1.612442 TCTTCTTCCCCACCCCTCG 60.612 63.158 0.00 0.00 0.00 4.63
979 1050 3.327404 TTCTTCCCCACCCCTCGC 61.327 66.667 0.00 0.00 0.00 5.03
1047 1147 0.254178 AACCGCCTCGTCCTACTCTA 59.746 55.000 0.00 0.00 0.00 2.43
1052 1152 1.165284 CCTCGTCCTACTCTACCGCC 61.165 65.000 0.00 0.00 0.00 6.13
1073 1173 3.204827 CGGCCCTCCTGCGATTTG 61.205 66.667 0.00 0.00 0.00 2.32
1458 1561 7.989416 TGGAACTATCGAAGGTTTGTTATTT 57.011 32.000 7.60 0.00 0.00 1.40
1460 1563 7.148540 TGGAACTATCGAAGGTTTGTTATTTCG 60.149 37.037 7.60 0.00 42.61 3.46
1462 1565 7.662604 ACTATCGAAGGTTTGTTATTTCGTT 57.337 32.000 0.00 0.95 42.08 3.85
1543 1671 4.212214 AGCGTTGAACAGATGAGTTTCTTC 59.788 41.667 0.00 0.00 0.00 2.87
1547 1675 3.394274 TGAACAGATGAGTTTCTTCCCCA 59.606 43.478 0.00 0.00 0.00 4.96
1551 1679 4.536090 ACAGATGAGTTTCTTCCCCACATA 59.464 41.667 0.00 0.00 0.00 2.29
1552 1680 5.192522 ACAGATGAGTTTCTTCCCCACATAT 59.807 40.000 0.00 0.00 0.00 1.78
1571 1699 8.289618 CCACATATAAGTAACGGATTTGATTGG 58.710 37.037 0.00 0.00 0.00 3.16
1639 1774 4.383770 CGGTGACTTTTCCACTACCCATAT 60.384 45.833 0.00 0.00 35.05 1.78
1653 1788 9.035890 CCACTACCCATATCTGTAATTATCTGA 57.964 37.037 0.00 0.00 0.00 3.27
1768 1903 4.381411 AGAAAGTTTTTCTACTGCGAGCT 58.619 39.130 2.39 0.00 0.00 4.09
1769 1904 5.539048 AGAAAGTTTTTCTACTGCGAGCTA 58.461 37.500 2.39 0.00 0.00 3.32
1985 2268 7.532682 TGTTTAACAACAGCTTCATTTTTCC 57.467 32.000 0.00 0.00 38.03 3.13
2122 2405 0.179065 TGCATCTCAATCTGCTCCCG 60.179 55.000 0.00 0.00 39.16 5.14
2127 2410 4.384056 CATCTCAATCTGCTCCCGTAAAT 58.616 43.478 0.00 0.00 0.00 1.40
2318 2622 9.221775 CAATCATACTTTGTTTCGTTAATAGCC 57.778 33.333 0.00 0.00 0.00 3.93
2349 2653 8.642432 TCTTTCTGTCTGAGATTCACTTCTTAA 58.358 33.333 0.00 0.00 0.00 1.85
2371 2675 6.538945 AAATTAGGCGTCATAAATTTGGGT 57.461 33.333 0.00 0.00 31.99 4.51
2400 2704 9.683069 ATTAATTGTTGACTAGCAAAGAAACAG 57.317 29.630 1.86 0.00 38.44 3.16
2467 2771 6.754675 GTCTTAGTCTGAACTCTGAATTAGGC 59.245 42.308 1.95 0.00 36.92 3.93
2496 2800 9.030452 AGATTCCTTGGATAGTATGTCTCATAC 57.970 37.037 10.71 10.71 0.00 2.39
2501 2805 5.645201 TGGATAGTATGTCTCATACTGCCT 58.355 41.667 23.95 13.30 36.38 4.75
2502 2806 6.077993 TGGATAGTATGTCTCATACTGCCTT 58.922 40.000 23.95 11.65 36.38 4.35
2588 3119 5.049336 GCTCATGTTCCATGAGATGATTCAG 60.049 44.000 29.17 8.54 46.25 3.02
2606 3137 4.524802 TCAGTAATGGCTTGATTGGGAT 57.475 40.909 0.00 0.00 0.00 3.85
2980 3557 7.313646 TCTGAACAATAGTCAAGTACTAGCAC 58.686 38.462 0.00 0.00 43.90 4.40
2993 3570 6.986904 AGTACTAGCACAAATTTAGAAGGC 57.013 37.500 0.00 0.00 0.00 4.35
3037 3614 4.859629 ATTTAGCTTCGGTTCGTCAATC 57.140 40.909 0.00 0.00 0.00 2.67
3053 3630 6.103997 TCGTCAATCACTAGTCATTAAACCC 58.896 40.000 0.00 0.00 0.00 4.11
3064 3641 1.405105 CATTAAACCCATGGACCTGCG 59.595 52.381 15.22 0.00 0.00 5.18
3076 3653 3.833645 CCTGCGTGGCCTAGCGTA 61.834 66.667 16.12 10.91 35.87 4.42
3089 3666 5.303589 TGGCCTAGCGTATACAGTATTTTCT 59.696 40.000 3.32 0.00 0.00 2.52
3135 3712 2.158460 CCTCCCTTTTATGTCCCCATCC 60.158 54.545 0.00 0.00 32.29 3.51
3138 3715 2.572290 CCTTTTATGTCCCCATCCGAC 58.428 52.381 0.00 0.00 32.29 4.79
3139 3716 2.572290 CTTTTATGTCCCCATCCGACC 58.428 52.381 0.00 0.00 32.29 4.79
3192 3769 3.617263 CGTCCTGCCACTACATACTTTTC 59.383 47.826 0.00 0.00 0.00 2.29
3239 3817 7.384115 TGCTGTTAGTAACACACTTTATCAGAC 59.616 37.037 11.75 0.00 38.80 3.51
3291 3869 6.985059 CCTAGAACTGGTAACACCTATTTAGC 59.015 42.308 0.00 0.00 46.17 3.09
3346 3926 7.793927 ATTTCTCTTGTTCCCGAGATAATTC 57.206 36.000 0.00 0.00 36.29 2.17
3352 3932 7.434492 TCTTGTTCCCGAGATAATTCATAGTC 58.566 38.462 0.00 0.00 0.00 2.59
3394 3976 3.392616 CCTTGCCTCATACCTCCAGTTAT 59.607 47.826 0.00 0.00 0.00 1.89
3399 3981 5.427157 TGCCTCATACCTCCAGTTATTGTAA 59.573 40.000 0.00 0.00 0.00 2.41
3514 4099 1.684248 GCTGTCATTGGCCCTCAATCT 60.684 52.381 0.00 0.00 43.70 2.40
3688 4273 9.787532 GTTGCTAGCATTATTGATTACTTTCAA 57.212 29.630 20.13 0.00 39.77 2.69
3814 4399 1.089920 CAGCCATTCCTCCAAACTCG 58.910 55.000 0.00 0.00 0.00 4.18
4282 4867 7.958180 ATGGAAGCAGTTTGCGTCTATCAAAA 61.958 38.462 14.72 0.00 46.14 2.44
4475 5060 9.274206 GTAATTACTCTGGTCTTTCTGTTTCTT 57.726 33.333 8.41 0.00 0.00 2.52
4513 5098 0.808847 GGAAGCCACCGAATACGTCC 60.809 60.000 0.00 0.00 37.88 4.79
4844 5438 3.319972 TGCTTTGCTCTGCTTCTTTGATT 59.680 39.130 0.00 0.00 0.00 2.57
5039 5635 5.047847 GGGCTTTCTTTAAACCTTTCACAC 58.952 41.667 0.00 0.00 0.00 3.82
5110 5706 5.507315 GGTTGTTTGGATTCTTGAACATCGT 60.507 40.000 0.00 0.00 32.64 3.73
5111 5707 5.766150 TGTTTGGATTCTTGAACATCGTT 57.234 34.783 0.00 0.00 0.00 3.85
5200 5804 5.303078 GCTACTCCAAGGATCTGTTCTATCA 59.697 44.000 0.00 0.00 0.00 2.15
5219 5823 7.220030 TCTATCATAGGTTTTCAATCTGGCTC 58.780 38.462 0.00 0.00 0.00 4.70
5234 5838 5.344743 TCTGGCTCGAATAAGAATTCAGT 57.655 39.130 8.44 0.00 41.44 3.41
5424 6052 5.504010 CGATGTTCTTTGCACACAGTAAGTT 60.504 40.000 0.00 0.00 0.00 2.66
5940 9306 3.953612 GGGATTTGTATGTTCAGCATCCA 59.046 43.478 0.00 0.00 38.94 3.41
6173 9566 2.753029 GGAGCAGTCAGGCTTGGT 59.247 61.111 0.00 0.00 45.99 3.67
6324 9735 4.994471 CTGCTGCTGCCGTCACCA 62.994 66.667 13.47 0.00 38.71 4.17
6592 10433 3.166489 ACTGAAGTAGATAACAGCGGC 57.834 47.619 0.00 0.00 34.25 6.53
6817 11127 3.947910 TTTCAACTCCGGTACTGTAGG 57.052 47.619 0.00 0.00 0.00 3.18
6949 12617 5.291971 AGTCGTACCAAACAGACGTAAATT 58.708 37.500 0.00 0.00 36.99 1.82
6969 12637 6.834959 AATTCAGCTGTAGAACGTATGATG 57.165 37.500 14.67 0.00 0.00 3.07
7155 15100 7.661536 ATATATATATCTCCAGCAACGTGGT 57.338 36.000 0.00 0.00 38.88 4.16
7156 15101 2.604046 ATATCTCCAGCAACGTGGTC 57.396 50.000 0.00 0.00 38.88 4.02
7158 15103 0.615331 ATCTCCAGCAACGTGGTCAT 59.385 50.000 0.00 0.00 38.88 3.06
7161 15106 2.159099 TCTCCAGCAACGTGGTCATATC 60.159 50.000 0.00 0.00 38.88 1.63
7162 15107 1.552792 TCCAGCAACGTGGTCATATCA 59.447 47.619 0.00 0.00 38.88 2.15
7166 15111 4.119136 CAGCAACGTGGTCATATCATACA 58.881 43.478 0.00 0.00 0.00 2.29
7168 15113 5.237127 CAGCAACGTGGTCATATCATACAAT 59.763 40.000 0.00 0.00 0.00 2.71
7169 15114 5.822519 AGCAACGTGGTCATATCATACAATT 59.177 36.000 0.00 0.00 0.00 2.32
7172 15117 8.289618 GCAACGTGGTCATATCATACAATTTAT 58.710 33.333 0.00 0.00 0.00 1.40
7211 16462 4.370917 TCCTACCAAACAGACGTAAACAC 58.629 43.478 0.00 0.00 0.00 3.32
7293 16544 1.300931 GACAGTCTTGCAGTGGCGA 60.301 57.895 0.00 0.00 45.35 5.54
7339 16595 0.402121 GCTCACTCCCCTTTCTGGTT 59.598 55.000 0.00 0.00 0.00 3.67
7367 16623 6.697019 CCACAAAACAGGTTACAGAAATCAAG 59.303 38.462 0.00 0.00 0.00 3.02
7376 16632 5.581085 GGTTACAGAAATCAAGTATGTCGCT 59.419 40.000 0.00 0.00 0.00 4.93
7387 16643 4.546829 AGTATGTCGCTTAGTCCCAAAA 57.453 40.909 0.00 0.00 0.00 2.44
7388 16644 4.504858 AGTATGTCGCTTAGTCCCAAAAG 58.495 43.478 0.00 0.00 0.00 2.27
7411 16669 2.437281 AGATTGCTAGTGGCTAGTGCAT 59.563 45.455 0.00 0.00 42.39 3.96
7442 16700 2.245159 TTCATGGGATCAGCGCTAAG 57.755 50.000 10.99 0.00 0.00 2.18
7490 16748 2.552373 GGGGATCACAAGGAAAGAACGT 60.552 50.000 0.00 0.00 0.00 3.99
7491 16749 2.484264 GGGATCACAAGGAAAGAACGTG 59.516 50.000 0.00 0.00 0.00 4.49
7497 16755 4.456222 TCACAAGGAAAGAACGTGACAAAA 59.544 37.500 0.00 0.00 31.92 2.44
7551 16810 5.071115 AGAGATTTGGGAGTAGAACATAGGC 59.929 44.000 0.00 0.00 0.00 3.93
7571 16830 2.103373 CCAGAGAAGACGAATGAGGGA 58.897 52.381 0.00 0.00 0.00 4.20
7576 16835 4.825085 AGAGAAGACGAATGAGGGAGATAC 59.175 45.833 0.00 0.00 0.00 2.24
7582 16841 3.322254 ACGAATGAGGGAGATACCATGTC 59.678 47.826 0.00 0.00 41.20 3.06
7619 16878 5.470368 TCTCCATCTCGAAATATTAAGGCG 58.530 41.667 0.00 0.00 0.00 5.52
7625 16884 2.937799 TCGAAATATTAAGGCGCGGTTT 59.062 40.909 8.83 0.00 0.00 3.27
7638 16897 2.666022 GCGCGGTTTGATTTTTATTGCT 59.334 40.909 8.83 0.00 0.00 3.91
7657 16916 3.202906 GCTTGGTTGATACGCTATTCCA 58.797 45.455 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.124736 GCTTAGGTGGCGATGGCA 60.125 61.111 1.01 0.00 42.47 4.92
11 12 2.423185 TCAATTTGCTTAGGTGGCGATG 59.577 45.455 0.00 0.00 0.00 3.84
21 22 0.810648 CTGCGGCCTCAATTTGCTTA 59.189 50.000 0.00 0.00 0.00 3.09
34 35 2.751436 TGGAGATTTGGCTGCGGC 60.751 61.111 9.72 9.72 37.82 6.53
35 36 1.372087 GAGTGGAGATTTGGCTGCGG 61.372 60.000 0.00 0.00 0.00 5.69
38 39 2.630158 CTCTGAGTGGAGATTTGGCTG 58.370 52.381 0.00 0.00 35.52 4.85
45 46 2.094286 CGTCAAAGCTCTGAGTGGAGAT 60.094 50.000 6.53 0.00 35.52 2.75
66 67 6.376018 AGGTGATAATAAGTCTAGATCGGAGC 59.624 42.308 0.00 0.00 0.00 4.70
86 87 4.104086 ACCATTGACTTGGATAGAGGTGA 58.896 43.478 0.00 0.00 39.25 4.02
90 91 4.406972 TCTGGACCATTGACTTGGATAGAG 59.593 45.833 0.00 0.00 39.25 2.43
95 97 3.874383 TTTCTGGACCATTGACTTGGA 57.126 42.857 0.00 0.00 39.25 3.53
101 103 3.117888 GGCCTCTATTTCTGGACCATTGA 60.118 47.826 0.00 0.00 0.00 2.57
102 104 3.217626 GGCCTCTATTTCTGGACCATTG 58.782 50.000 0.00 0.00 0.00 2.82
103 105 2.852449 TGGCCTCTATTTCTGGACCATT 59.148 45.455 3.32 0.00 0.00 3.16
109 111 7.009179 TCTATGTATTGGCCTCTATTTCTGG 57.991 40.000 3.32 0.00 0.00 3.86
116 118 4.082190 GCGTGATCTATGTATTGGCCTCTA 60.082 45.833 3.32 0.00 0.00 2.43
120 123 2.766313 TGCGTGATCTATGTATTGGCC 58.234 47.619 0.00 0.00 0.00 5.36
121 124 3.996363 TGATGCGTGATCTATGTATTGGC 59.004 43.478 0.00 0.00 31.55 4.52
126 129 7.214467 TCTATGTTGATGCGTGATCTATGTA 57.786 36.000 0.00 0.00 31.55 2.29
128 131 6.128715 GGTTCTATGTTGATGCGTGATCTATG 60.129 42.308 0.00 0.00 31.55 2.23
141 144 5.620206 ACACAATGTGAGGTTCTATGTTGA 58.380 37.500 21.34 0.00 36.96 3.18
144 147 4.690748 CGAACACAATGTGAGGTTCTATGT 59.309 41.667 21.34 0.00 36.96 2.29
145 148 4.929211 TCGAACACAATGTGAGGTTCTATG 59.071 41.667 21.34 2.00 36.96 2.23
146 149 4.929808 GTCGAACACAATGTGAGGTTCTAT 59.070 41.667 21.34 0.00 36.96 1.98
147 150 4.304110 GTCGAACACAATGTGAGGTTCTA 58.696 43.478 21.34 3.05 36.96 2.10
149 152 2.096909 CGTCGAACACAATGTGAGGTTC 60.097 50.000 21.34 12.17 36.96 3.62
151 154 1.202486 ACGTCGAACACAATGTGAGGT 60.202 47.619 21.34 6.36 36.96 3.85
153 156 3.734231 ACTAACGTCGAACACAATGTGAG 59.266 43.478 21.34 10.69 36.96 3.51
157 160 3.362596 CCACACTAACGTCGAACACAATG 60.363 47.826 0.00 0.00 0.00 2.82
158 161 2.798283 CCACACTAACGTCGAACACAAT 59.202 45.455 0.00 0.00 0.00 2.71
161 164 1.843992 ACCACACTAACGTCGAACAC 58.156 50.000 0.00 0.00 0.00 3.32
163 166 3.371168 TGTAACCACACTAACGTCGAAC 58.629 45.455 0.00 0.00 0.00 3.95
164 167 3.706802 TGTAACCACACTAACGTCGAA 57.293 42.857 0.00 0.00 0.00 3.71
165 168 3.181492 TGTTGTAACCACACTAACGTCGA 60.181 43.478 0.00 0.00 33.30 4.20
167 170 4.362279 TCTGTTGTAACCACACTAACGTC 58.638 43.478 0.00 0.00 33.30 4.34
168 171 4.389890 TCTGTTGTAACCACACTAACGT 57.610 40.909 0.00 0.00 33.30 3.99
169 172 4.748102 ACATCTGTTGTAACCACACTAACG 59.252 41.667 0.00 0.00 36.57 3.18
170 173 6.702723 TGTACATCTGTTGTAACCACACTAAC 59.297 38.462 0.00 0.00 42.37 2.34
171 174 6.702723 GTGTACATCTGTTGTAACCACACTAA 59.297 38.462 0.00 0.00 42.37 2.24
172 175 6.183360 TGTGTACATCTGTTGTAACCACACTA 60.183 38.462 17.04 7.10 41.51 2.74
177 180 7.392494 TTTTTGTGTACATCTGTTGTAACCA 57.608 32.000 0.00 0.00 42.37 3.67
178 181 6.915843 CCTTTTTGTGTACATCTGTTGTAACC 59.084 38.462 0.00 0.00 42.37 2.85
179 182 7.699566 TCCTTTTTGTGTACATCTGTTGTAAC 58.300 34.615 0.00 3.37 42.37 2.50
180 183 7.867305 TCCTTTTTGTGTACATCTGTTGTAA 57.133 32.000 0.00 0.00 42.37 2.41
181 184 9.733556 ATATCCTTTTTGTGTACATCTGTTGTA 57.266 29.630 0.00 0.00 39.87 2.41
186 189 8.279970 TCCAATATCCTTTTTGTGTACATCTG 57.720 34.615 0.00 0.00 0.00 2.90
190 193 8.952278 GTGTATCCAATATCCTTTTTGTGTACA 58.048 33.333 0.00 0.00 0.00 2.90
213 219 1.751924 GAGATGGTAGAAGCGGAGTGT 59.248 52.381 0.00 0.00 0.00 3.55
218 224 0.312416 CTCCGAGATGGTAGAAGCGG 59.688 60.000 0.00 0.00 39.52 5.52
239 245 0.504384 GCACGATTGTCGGATCATCG 59.496 55.000 16.00 16.00 45.59 3.84
242 248 0.177836 ATGGCACGATTGTCGGATCA 59.822 50.000 4.28 0.00 45.59 2.92
246 252 1.449423 TGGATGGCACGATTGTCGG 60.449 57.895 4.28 0.00 45.59 4.79
253 259 0.107643 TTGTGAAGTGGATGGCACGA 59.892 50.000 0.00 0.00 34.12 4.35
255 261 1.001378 GTGTTGTGAAGTGGATGGCAC 60.001 52.381 0.00 0.00 0.00 5.01
267 273 2.354188 CTCGTCGGCGTGTTGTGA 60.354 61.111 10.18 0.00 39.49 3.58
272 278 4.702081 GCAGTCTCGTCGGCGTGT 62.702 66.667 10.18 0.00 39.49 4.49
280 289 3.812019 CGTAGGCGGCAGTCTCGT 61.812 66.667 13.08 0.00 32.57 4.18
310 319 4.891727 AGATTGGTAGGCCGCGCG 62.892 66.667 25.67 25.67 37.67 6.86
313 322 0.685097 TATGGAGATTGGTAGGCCGC 59.315 55.000 0.00 0.00 37.67 6.53
314 323 3.338249 CATTATGGAGATTGGTAGGCCG 58.662 50.000 0.00 0.00 37.67 6.13
322 331 2.497138 TGGCGAGCATTATGGAGATTG 58.503 47.619 0.00 0.00 0.00 2.67
334 343 4.424711 GGGGGAACATGGCGAGCA 62.425 66.667 0.00 0.00 0.00 4.26
352 361 1.300465 CCAGATCCGATGCACTCCG 60.300 63.158 0.00 0.00 0.00 4.63
354 363 1.596477 GCCCAGATCCGATGCACTC 60.596 63.158 0.00 0.00 0.00 3.51
355 364 2.321263 CTGCCCAGATCCGATGCACT 62.321 60.000 0.00 0.00 0.00 4.40
356 365 1.890979 CTGCCCAGATCCGATGCAC 60.891 63.158 0.00 0.00 0.00 4.57
357 366 2.507452 CTGCCCAGATCCGATGCA 59.493 61.111 0.00 0.00 0.00 3.96
358 367 2.976903 GCTGCCCAGATCCGATGC 60.977 66.667 0.00 0.00 0.00 3.91
359 368 1.072678 ATGCTGCCCAGATCCGATG 59.927 57.895 0.00 0.00 0.00 3.84
360 369 1.072678 CATGCTGCCCAGATCCGAT 59.927 57.895 0.00 0.00 0.00 4.18
362 371 2.593725 CCATGCTGCCCAGATCCG 60.594 66.667 0.00 0.00 0.00 4.18
363 372 2.203451 CCCATGCTGCCCAGATCC 60.203 66.667 0.00 0.00 0.00 3.36
377 386 1.376683 GCGACATACTTGGCACCCA 60.377 57.895 0.00 0.00 0.00 4.51
378 387 2.112815 GGCGACATACTTGGCACCC 61.113 63.158 0.00 0.00 0.00 4.61
396 405 4.360405 CTTTGGGGTGGTCGGGGG 62.360 72.222 0.00 0.00 0.00 5.40
421 432 3.684990 TGCGGCAGAGAAGAGCGT 61.685 61.111 0.00 0.00 0.00 5.07
430 441 1.220749 GTTATCAGGGTGCGGCAGA 59.779 57.895 1.18 0.00 0.00 4.26
433 444 1.993369 GCTTGTTATCAGGGTGCGGC 61.993 60.000 0.00 0.00 0.00 6.53
435 446 0.739462 TCGCTTGTTATCAGGGTGCG 60.739 55.000 0.00 0.00 42.70 5.34
436 447 0.727398 GTCGCTTGTTATCAGGGTGC 59.273 55.000 0.00 0.00 0.00 5.01
438 449 0.739813 GCGTCGCTTGTTATCAGGGT 60.740 55.000 10.68 0.00 0.00 4.34
440 451 1.752501 CGGCGTCGCTTGTTATCAGG 61.753 60.000 18.11 0.00 0.00 3.86
441 452 1.631072 CGGCGTCGCTTGTTATCAG 59.369 57.895 18.11 0.00 0.00 2.90
442 453 3.775314 CGGCGTCGCTTGTTATCA 58.225 55.556 18.11 0.00 0.00 2.15
454 467 4.204799 TCTAGATATATACATGGCGGCGT 58.795 43.478 9.37 0.00 0.00 5.68
486 500 6.042143 AGTGTTCATGTGGTTGAATTTGTTC 58.958 36.000 0.00 0.00 37.88 3.18
518 532 7.255801 GGTCTGGTCATGGAGAATTTTGTTTTA 60.256 37.037 0.00 0.00 0.00 1.52
707 747 2.752238 AGGAGGCGGAGACACTCG 60.752 66.667 0.00 0.00 39.87 4.18
800 845 1.154488 GCGTGTTGTATGGTGCGTG 60.154 57.895 0.00 0.00 0.00 5.34
803 857 1.434555 TGTAGCGTGTTGTATGGTGC 58.565 50.000 0.00 0.00 0.00 5.01
805 859 2.419574 GGGATGTAGCGTGTTGTATGGT 60.420 50.000 0.00 0.00 0.00 3.55
809 863 1.404986 GCAGGGATGTAGCGTGTTGTA 60.405 52.381 0.00 0.00 0.00 2.41
811 865 1.695893 CGCAGGGATGTAGCGTGTTG 61.696 60.000 0.00 0.00 45.82 3.33
812 866 1.447838 CGCAGGGATGTAGCGTGTT 60.448 57.895 0.00 0.00 45.82 3.32
813 867 2.184322 CGCAGGGATGTAGCGTGT 59.816 61.111 0.00 0.00 45.82 4.49
817 871 4.530857 ACGGCGCAGGGATGTAGC 62.531 66.667 13.26 0.00 0.00 3.58
818 872 2.173669 CAACGGCGCAGGGATGTAG 61.174 63.158 13.26 0.00 0.00 2.74
819 873 2.125310 CAACGGCGCAGGGATGTA 60.125 61.111 13.26 0.00 0.00 2.29
820 874 4.329545 ACAACGGCGCAGGGATGT 62.330 61.111 13.26 10.96 0.00 3.06
821 875 3.499737 GACAACGGCGCAGGGATG 61.500 66.667 13.26 10.31 0.00 3.51
822 876 3.958147 CTGACAACGGCGCAGGGAT 62.958 63.158 13.26 0.00 0.00 3.85
823 877 4.680237 CTGACAACGGCGCAGGGA 62.680 66.667 13.26 0.00 0.00 4.20
824 878 4.988598 ACTGACAACGGCGCAGGG 62.989 66.667 13.26 6.20 34.05 4.45
825 879 3.414700 GACTGACAACGGCGCAGG 61.415 66.667 13.26 4.07 34.05 4.85
826 880 3.414700 GGACTGACAACGGCGCAG 61.415 66.667 10.83 8.25 35.81 5.18
827 881 4.980805 GGGACTGACAACGGCGCA 62.981 66.667 10.83 0.00 0.00 6.09
829 883 4.657824 ACGGGACTGACAACGGCG 62.658 66.667 4.80 4.80 0.00 6.46
830 884 2.280592 AACGGGACTGACAACGGC 60.281 61.111 0.00 0.00 0.00 5.68
831 885 1.959226 CCAACGGGACTGACAACGG 60.959 63.158 0.00 0.00 35.59 4.44
832 886 1.068417 TCCAACGGGACTGACAACG 59.932 57.895 0.00 0.00 38.64 4.10
841 895 2.449967 TAGCAGGGAGTCCAACGGGA 62.450 60.000 12.30 0.00 42.29 5.14
861 916 2.106332 GGCGTGGGAATCGTCGAT 59.894 61.111 0.75 0.75 0.00 3.59
890 949 1.301293 GCCTGGGAGGGTGAAAGAG 59.699 63.158 0.00 0.00 35.37 2.85
923 988 1.454847 CTCTCCCCGTCTCCCTCTG 60.455 68.421 0.00 0.00 0.00 3.35
927 992 2.835895 GAGCTCTCCCCGTCTCCC 60.836 72.222 6.43 0.00 0.00 4.30
1543 1671 6.292923 TCAAATCCGTTACTTATATGTGGGG 58.707 40.000 1.63 1.13 0.00 4.96
1547 1675 9.621629 TTCCAATCAAATCCGTTACTTATATGT 57.378 29.630 0.00 0.00 0.00 2.29
1551 1679 8.575649 AAGTTCCAATCAAATCCGTTACTTAT 57.424 30.769 0.00 0.00 0.00 1.73
1552 1680 7.989416 AAGTTCCAATCAAATCCGTTACTTA 57.011 32.000 0.00 0.00 0.00 2.24
1571 1699 2.224354 TGGGGTCGTGAAAGGTAAGTTC 60.224 50.000 0.00 0.00 0.00 3.01
1639 1774 7.994911 ACATGCTTCCAATCAGATAATTACAGA 59.005 33.333 0.00 0.00 0.00 3.41
1768 1903 6.954487 TTCTAACTCAATGGAGCTATCGTA 57.046 37.500 0.00 0.00 45.42 3.43
1769 1904 5.854010 TTCTAACTCAATGGAGCTATCGT 57.146 39.130 0.00 0.00 45.42 3.73
1985 2268 8.890718 TCATGCTGAGATCTCAATAAAGAAAAG 58.109 33.333 25.09 11.18 39.39 2.27
2122 2405 6.959871 GGCGACTACTTTTGCTCTTTATTTAC 59.040 38.462 0.00 0.00 0.00 2.01
2127 2410 3.744426 GTGGCGACTACTTTTGCTCTTTA 59.256 43.478 0.00 0.00 0.00 1.85
2135 2418 4.444536 TGTAACAAGTGGCGACTACTTTT 58.555 39.130 0.30 0.00 36.29 2.27
2308 2612 4.387862 ACAGAAAGACAACGGCTATTAACG 59.612 41.667 0.00 0.00 0.00 3.18
2315 2619 1.412710 TCAGACAGAAAGACAACGGCT 59.587 47.619 0.00 0.00 0.00 5.52
2318 2622 4.984785 TGAATCTCAGACAGAAAGACAACG 59.015 41.667 0.00 0.00 33.62 4.10
2349 2653 5.654650 TCACCCAAATTTATGACGCCTAATT 59.345 36.000 0.00 0.00 0.00 1.40
2400 2704 4.872691 AGTGATATTACAGTGCAGCTCAAC 59.127 41.667 0.00 0.00 0.00 3.18
2588 3119 5.324409 TCCATATCCCAATCAAGCCATTAC 58.676 41.667 0.00 0.00 0.00 1.89
2606 3137 3.788227 AGCACAGTTGGTTTCTCCATA 57.212 42.857 0.00 0.00 46.60 2.74
2968 3545 7.119846 AGCCTTCTAAATTTGTGCTAGTACTTG 59.880 37.037 12.42 0.00 0.00 3.16
2980 3557 9.771534 AGCTACTATAAGAGCCTTCTAAATTTG 57.228 33.333 0.00 0.00 39.65 2.32
3037 3614 4.881850 GGTCCATGGGTTTAATGACTAGTG 59.118 45.833 13.02 0.00 0.00 2.74
3053 3630 2.930385 CTAGGCCACGCAGGTCCATG 62.930 65.000 5.01 0.00 45.84 3.66
3064 3641 4.516365 AATACTGTATACGCTAGGCCAC 57.484 45.455 5.01 0.00 0.00 5.01
3089 3666 6.430925 GTGGCTATCCATACTGAATGCATTTA 59.569 38.462 14.33 8.72 45.62 1.40
3104 3681 1.681229 AAAAGGGAGGTGGCTATCCA 58.319 50.000 5.74 0.00 40.85 3.41
3135 3712 5.643777 ACTCTTCATCCAAAAACATAGGTCG 59.356 40.000 0.00 0.00 0.00 4.79
3171 3748 4.833390 AGAAAAGTATGTAGTGGCAGGAC 58.167 43.478 0.00 0.00 0.00 3.85
3192 3769 6.700081 CAGCACCAATCATTTATCAATGGAAG 59.300 38.462 0.00 0.00 40.41 3.46
3207 3785 4.755123 AGTGTGTTACTAACAGCACCAATC 59.245 41.667 19.91 4.20 43.10 2.67
3211 3789 6.425721 TGATAAAGTGTGTTACTAACAGCACC 59.574 38.462 19.91 11.62 43.10 5.01
3239 3817 4.696479 AATAGGCTGGTCTATGGAAGTG 57.304 45.455 0.00 0.00 31.01 3.16
3380 3961 9.530633 GTCTTACTTACAATAACTGGAGGTATG 57.469 37.037 0.00 0.00 30.86 2.39
3394 3976 7.581476 GCAATTAGCAACTGTCTTACTTACAA 58.419 34.615 0.00 0.00 44.79 2.41
3514 4099 3.718434 AGATGACATGGCCTATTCCAGAA 59.282 43.478 3.32 0.00 39.89 3.02
3631 4216 6.403636 GCATTTGGAAGTAGTCACTTATGGTG 60.404 42.308 0.00 0.00 45.18 4.17
3688 4273 6.506538 AATATAGCAGTCACCTCTTTCCAT 57.493 37.500 0.00 0.00 0.00 3.41
3814 4399 6.446781 ACATCATTGATCAAATCTGTGTCC 57.553 37.500 13.09 0.00 0.00 4.02
4282 4867 8.274322 TGATCACCACCATCAAATATCTTAAGT 58.726 33.333 1.63 0.00 0.00 2.24
4513 5098 0.528249 GCAACTGTTGGGCACTTGTG 60.528 55.000 21.01 0.00 0.00 3.33
4981 5577 1.795768 CTTTTCTCACTGGCGCTACA 58.204 50.000 7.64 0.00 0.00 2.74
5039 5635 4.748892 CCTGTTACACACCACATCTCTAG 58.251 47.826 0.00 0.00 0.00 2.43
5110 5706 3.769844 AGCCTCGAAACTCCTCATTAGAA 59.230 43.478 0.00 0.00 0.00 2.10
5111 5707 3.366396 AGCCTCGAAACTCCTCATTAGA 58.634 45.455 0.00 0.00 0.00 2.10
5200 5804 4.487714 TCGAGCCAGATTGAAAACCTAT 57.512 40.909 0.00 0.00 0.00 2.57
5234 5838 6.721318 ACCACTTTGGCTCTCTTCATTATTA 58.279 36.000 0.00 0.00 42.67 0.98
5279 5883 6.463360 ACAAAACAATTGGTGAGAACAAAGT 58.537 32.000 10.83 0.00 0.00 2.66
6173 9566 2.660064 GCCCCAGAAGCTTCCGAGA 61.660 63.158 22.81 0.00 0.00 4.04
6324 9735 1.636148 ATTTGAGCAATGGTGGCAGT 58.364 45.000 0.00 0.00 0.00 4.40
6592 10433 9.599866 TTATGAATCCTACAAGTGTCAAGTATG 57.400 33.333 0.00 0.00 0.00 2.39
6761 10604 7.607991 CCATCTACATACTCACTTTGGAAAAGT 59.392 37.037 0.00 0.00 0.00 2.66
6949 12617 3.381590 AGCATCATACGTTCTACAGCTGA 59.618 43.478 23.35 2.95 0.00 4.26
6969 12637 0.035739 TAACCAGTTCGGGGTTCAGC 59.964 55.000 0.00 0.00 45.26 4.26
7142 15087 1.552792 TGATATGACCACGTTGCTGGA 59.447 47.619 0.00 0.00 35.04 3.86
7143 15088 2.022764 TGATATGACCACGTTGCTGG 57.977 50.000 0.00 0.00 37.33 4.85
7144 15089 4.119136 TGTATGATATGACCACGTTGCTG 58.881 43.478 0.00 0.00 0.00 4.41
7145 15090 4.400529 TGTATGATATGACCACGTTGCT 57.599 40.909 0.00 0.00 0.00 3.91
7166 15111 9.539194 AGGATTCAGAAACTGGAGAAATAAATT 57.461 29.630 0.00 0.00 31.51 1.82
7168 15113 9.449719 GTAGGATTCAGAAACTGGAGAAATAAA 57.550 33.333 0.00 0.00 31.51 1.40
7169 15114 8.047310 GGTAGGATTCAGAAACTGGAGAAATAA 58.953 37.037 0.00 0.00 31.51 1.40
7172 15117 5.309543 TGGTAGGATTCAGAAACTGGAGAAA 59.690 40.000 0.00 0.00 31.51 2.52
7175 15120 4.826274 TGGTAGGATTCAGAAACTGGAG 57.174 45.455 0.00 0.00 31.51 3.86
7176 15121 5.163141 TGTTTGGTAGGATTCAGAAACTGGA 60.163 40.000 0.00 0.00 31.51 3.86
7177 15122 5.070001 TGTTTGGTAGGATTCAGAAACTGG 58.930 41.667 0.00 0.00 31.51 4.00
7179 15124 5.998363 GTCTGTTTGGTAGGATTCAGAAACT 59.002 40.000 0.00 0.00 34.49 2.66
7180 15125 5.107065 CGTCTGTTTGGTAGGATTCAGAAAC 60.107 44.000 0.00 0.00 34.49 2.78
7181 15126 4.994852 CGTCTGTTTGGTAGGATTCAGAAA 59.005 41.667 0.00 0.00 34.49 2.52
7182 15127 4.039973 ACGTCTGTTTGGTAGGATTCAGAA 59.960 41.667 0.00 0.00 34.49 3.02
7185 15130 5.471556 TTACGTCTGTTTGGTAGGATTCA 57.528 39.130 0.00 0.00 0.00 2.57
7186 15131 5.697633 TGTTTACGTCTGTTTGGTAGGATTC 59.302 40.000 0.00 0.00 0.00 2.52
7211 16462 0.597637 GGATGATACTGTCCGCACCG 60.598 60.000 0.00 0.00 0.00 4.94
7339 16595 4.764050 TCTGTAACCTGTTTTGTGGAGA 57.236 40.909 0.00 0.00 0.00 3.71
7367 16623 3.063588 GCTTTTGGGACTAAGCGACATAC 59.936 47.826 0.00 0.00 37.08 2.39
7387 16643 5.855596 GCACTAGCCACTAGCAATCTGCT 62.856 52.174 6.38 6.38 45.81 4.24
7411 16669 7.441157 CGCTGATCCCATGAATAAGTTTAGTAA 59.559 37.037 0.00 0.00 0.00 2.24
7442 16700 7.637631 AAGAAGAAGCAGAATATTTTCCTCC 57.362 36.000 0.00 0.00 31.84 4.30
7551 16810 2.100584 CTCCCTCATTCGTCTTCTCTGG 59.899 54.545 0.00 0.00 0.00 3.86
7571 16830 4.081420 AGAGTGCTTTTCGACATGGTATCT 60.081 41.667 0.00 0.00 0.00 1.98
7576 16835 3.499918 AGAAAGAGTGCTTTTCGACATGG 59.500 43.478 0.00 0.00 44.10 3.66
7582 16841 3.999663 AGATGGAGAAAGAGTGCTTTTCG 59.000 43.478 0.00 0.00 44.10 3.46
7619 16878 4.450757 ACCAAGCAATAAAAATCAAACCGC 59.549 37.500 0.00 0.00 0.00 5.68
7625 16884 6.529829 GCGTATCAACCAAGCAATAAAAATCA 59.470 34.615 0.00 0.00 0.00 2.57
7638 16897 5.680619 AGAATGGAATAGCGTATCAACCAA 58.319 37.500 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.