Multiple sequence alignment - TraesCS1A01G084400

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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 TraesCS1A01G084400 chr1A 100.000 1914 0 0 635 2548 70699489 70697576 0.000000e+00 3535.0
1 TraesCS1A01G084400 chr1A 100.000 443 0 0 1 443 70700123 70699681 0.000000e+00 819.0
2 TraesCS1A01G084400 chr1A 86.538 156 16 4 128 281 37618699 37618547 1.570000e-37 167.0
3 TraesCS1A01G084400 chr1D 93.144 773 40 9 1784 2548 70341756 70340989 0.000000e+00 1122.0
4 TraesCS1A01G084400 chr2B 90.533 750 51 5 1051 1783 167511331 167512077 0.000000e+00 974.0
5 TraesCS1A01G084400 chr2B 85.714 175 18 7 128 299 214277143 214277313 7.240000e-41 178.0
6 TraesCS1A01G084400 chr1B 89.960 747 55 5 1051 1780 273481379 273482122 0.000000e+00 946.0
7 TraesCS1A01G084400 chr1B 89.720 749 58 12 1051 1783 273615932 273616677 0.000000e+00 939.0
8 TraesCS1A01G084400 chr1B 89.481 751 59 8 1052 1785 569883746 569884493 0.000000e+00 931.0
9 TraesCS1A01G084400 chr1B 88.400 750 67 11 1051 1782 593243003 593243750 0.000000e+00 885.0
10 TraesCS1A01G084400 chr1B 88.032 752 66 14 1051 1783 647924422 647923676 0.000000e+00 869.0
11 TraesCS1A01G084400 chr1B 87.666 754 67 14 1051 1783 566182578 566181830 0.000000e+00 854.0
12 TraesCS1A01G084400 chr1B 90.935 353 22 1 2194 2546 111666965 111666623 1.380000e-127 466.0
13 TraesCS1A01G084400 chr1B 90.964 332 24 3 1784 2112 111667338 111667010 2.330000e-120 442.0
14 TraesCS1A01G084400 chr1B 89.714 350 29 3 708 1056 105289457 105289114 8.370000e-120 440.0
15 TraesCS1A01G084400 chr1B 88.095 168 17 2 892 1056 58915208 58915041 2.000000e-46 196.0
16 TraesCS1A01G084400 chr1B 86.826 167 21 1 891 1056 273613629 273613795 4.330000e-43 185.0
17 TraesCS1A01G084400 chr1B 86.228 167 22 1 891 1056 273479128 273479294 2.010000e-41 180.0
18 TraesCS1A01G084400 chr1B 90.722 97 9 0 1 97 111667436 111667340 2.060000e-26 130.0
19 TraesCS1A01G084400 chr6D 89.600 750 56 6 1051 1783 436381915 436382659 0.000000e+00 933.0
20 TraesCS1A01G084400 chr6D 85.380 171 20 2 891 1056 436380444 436380614 3.370000e-39 172.0
21 TraesCS1A01G084400 chr6D 95.122 41 1 1 722 762 100198998 100198959 2.120000e-06 63.9
22 TraesCS1A01G084400 chr5B 89.418 756 55 6 1051 1783 438898252 438897499 0.000000e+00 929.0
23 TraesCS1A01G084400 chrUn 88.830 752 63 9 1051 1783 303151841 303151092 0.000000e+00 904.0
24 TraesCS1A01G084400 chrUn 88.697 752 64 9 1051 1783 71429013 71428264 0.000000e+00 898.0
25 TraesCS1A01G084400 chrUn 88.564 752 65 9 1051 1783 71486677 71485928 0.000000e+00 893.0
26 TraesCS1A01G084400 chrUn 89.091 605 47 8 1051 1638 291953390 291952788 0.000000e+00 734.0
27 TraesCS1A01G084400 chr3D 88.598 763 62 12 1051 1795 342804742 342803987 0.000000e+00 904.0
28 TraesCS1A01G084400 chr7D 88.446 753 65 12 1051 1784 228976466 228975717 0.000000e+00 889.0
29 TraesCS1A01G084400 chr7D 82.288 271 29 17 127 383 69496075 69495810 1.540000e-52 217.0
30 TraesCS1A01G084400 chr7A 88.462 754 63 10 1051 1783 711780435 711779685 0.000000e+00 889.0
31 TraesCS1A01G084400 chr7B 87.899 752 69 10 1051 1783 740166715 740167463 0.000000e+00 865.0
32 TraesCS1A01G084400 chr7B 82.562 281 25 13 763 1023 15746088 15745812 2.550000e-55 226.0
33 TraesCS1A01G084400 chr7B 79.643 280 34 16 129 403 716283572 716283311 2.010000e-41 180.0
34 TraesCS1A01G084400 chr7B 79.537 259 36 14 121 375 122951763 122952008 4.360000e-38 169.0
35 TraesCS1A01G084400 chr7B 78.764 259 38 14 121 375 123029780 123030025 9.440000e-35 158.0
36 TraesCS1A01G084400 chr4D 87.517 753 57 13 1051 1784 248924669 248923935 0.000000e+00 835.0
37 TraesCS1A01G084400 chr4D 80.866 277 32 16 129 401 493930105 493929846 5.560000e-47 198.0
38 TraesCS1A01G084400 chr4D 95.122 41 1 1 722 762 329012134 329012173 2.120000e-06 63.9
39 TraesCS1A01G084400 chr3A 91.515 165 12 2 892 1055 750314879 750315042 2.550000e-55 226.0
40 TraesCS1A01G084400 chr3A 88.690 168 18 1 891 1057 456407404 456407571 1.200000e-48 204.0
41 TraesCS1A01G084400 chr4B 80.142 282 34 15 129 403 435169688 435169954 9.300000e-45 191.0
42 TraesCS1A01G084400 chr5D 87.898 157 15 4 129 285 544775828 544775980 5.600000e-42 182.0
43 TraesCS1A01G084400 chr3B 90.511 137 13 0 887 1023 515472953 515472817 5.600000e-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 TraesCS1A01G084400 chr1A 70697576 70700123 2547 True 2177.0 3535 100.000000 1 2548 2 chr1A.!!$R2 2547
1 TraesCS1A01G084400 chr1D 70340989 70341756 767 True 1122.0 1122 93.144000 1784 2548 1 chr1D.!!$R1 764
2 TraesCS1A01G084400 chr2B 167511331 167512077 746 False 974.0 974 90.533000 1051 1783 1 chr2B.!!$F1 732
3 TraesCS1A01G084400 chr1B 569883746 569884493 747 False 931.0 931 89.481000 1052 1785 1 chr1B.!!$F1 733
4 TraesCS1A01G084400 chr1B 593243003 593243750 747 False 885.0 885 88.400000 1051 1782 1 chr1B.!!$F2 731
5 TraesCS1A01G084400 chr1B 647923676 647924422 746 True 869.0 869 88.032000 1051 1783 1 chr1B.!!$R4 732
6 TraesCS1A01G084400 chr1B 566181830 566182578 748 True 854.0 854 87.666000 1051 1783 1 chr1B.!!$R3 732
7 TraesCS1A01G084400 chr1B 273479128 273482122 2994 False 563.0 946 88.094000 891 1780 2 chr1B.!!$F3 889
8 TraesCS1A01G084400 chr1B 273613629 273616677 3048 False 562.0 939 88.273000 891 1783 2 chr1B.!!$F4 892
9 TraesCS1A01G084400 chr1B 111666623 111667436 813 True 346.0 466 90.873667 1 2546 3 chr1B.!!$R5 2545
10 TraesCS1A01G084400 chr6D 436380444 436382659 2215 False 552.5 933 87.490000 891 1783 2 chr6D.!!$F1 892
11 TraesCS1A01G084400 chr5B 438897499 438898252 753 True 929.0 929 89.418000 1051 1783 1 chr5B.!!$R1 732
12 TraesCS1A01G084400 chrUn 303151092 303151841 749 True 904.0 904 88.830000 1051 1783 1 chrUn.!!$R4 732
13 TraesCS1A01G084400 chrUn 71428264 71429013 749 True 898.0 898 88.697000 1051 1783 1 chrUn.!!$R1 732
14 TraesCS1A01G084400 chrUn 71485928 71486677 749 True 893.0 893 88.564000 1051 1783 1 chrUn.!!$R2 732
15 TraesCS1A01G084400 chrUn 291952788 291953390 602 True 734.0 734 89.091000 1051 1638 1 chrUn.!!$R3 587
16 TraesCS1A01G084400 chr3D 342803987 342804742 755 True 904.0 904 88.598000 1051 1795 1 chr3D.!!$R1 744
17 TraesCS1A01G084400 chr7D 228975717 228976466 749 True 889.0 889 88.446000 1051 1784 1 chr7D.!!$R2 733
18 TraesCS1A01G084400 chr7A 711779685 711780435 750 True 889.0 889 88.462000 1051 1783 1 chr7A.!!$R1 732
19 TraesCS1A01G084400 chr7B 740166715 740167463 748 False 865.0 865 87.899000 1051 1783 1 chr7B.!!$F3 732
20 TraesCS1A01G084400 chr4D 248923935 248924669 734 True 835.0 835 87.517000 1051 1784 1 chr4D.!!$R1 733

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
370 371 0.113776 ACCTCACCTGACGAACCCTA 59.886 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 4094 0.607489 CATAGGCCCATAGCTGTGGC 60.607 60.0 23.35 17.74 44.59 5.01 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
79 80 3.181475 TGAACAGACTTGACTGGACAGAC 60.181 47.826 6.29 0.20 41.59 3.51
84 85 3.320541 AGACTTGACTGGACAGACAGAAG 59.679 47.826 6.29 4.42 40.97 2.85
97 98 1.822371 GACAGAAGAGAGGGACTGGAC 59.178 57.143 0.00 0.00 41.55 4.02
98 99 1.148027 ACAGAAGAGAGGGACTGGACA 59.852 52.381 0.00 0.00 41.55 4.02
99 100 1.824230 CAGAAGAGAGGGACTGGACAG 59.176 57.143 0.00 0.00 41.55 3.51
100 101 1.713647 AGAAGAGAGGGACTGGACAGA 59.286 52.381 6.29 0.00 41.55 3.41
101 102 1.822371 GAAGAGAGGGACTGGACAGAC 59.178 57.143 6.29 0.00 41.55 3.51
102 103 0.780637 AGAGAGGGACTGGACAGACA 59.219 55.000 6.29 0.00 41.55 3.41
103 104 1.181786 GAGAGGGACTGGACAGACAG 58.818 60.000 6.29 0.00 41.55 3.51
104 105 0.780637 AGAGGGACTGGACAGACAGA 59.219 55.000 6.29 0.00 41.55 3.41
105 106 1.148027 AGAGGGACTGGACAGACAGAA 59.852 52.381 6.29 0.00 41.55 3.02
106 107 1.548269 GAGGGACTGGACAGACAGAAG 59.452 57.143 6.29 0.00 41.55 2.85
107 108 1.148027 AGGGACTGGACAGACAGAAGA 59.852 52.381 6.29 0.00 40.97 2.87
108 109 1.548269 GGGACTGGACAGACAGAAGAG 59.452 57.143 6.29 0.00 40.97 2.85
109 110 2.520069 GGACTGGACAGACAGAAGAGA 58.480 52.381 6.29 0.00 40.97 3.10
110 111 2.491693 GGACTGGACAGACAGAAGAGAG 59.508 54.545 6.29 0.00 40.97 3.20
111 112 2.491693 GACTGGACAGACAGAAGAGAGG 59.508 54.545 6.29 0.00 40.97 3.69
112 113 1.824230 CTGGACAGACAGAAGAGAGGG 59.176 57.143 0.00 0.00 40.97 4.30
113 114 1.429299 TGGACAGACAGAAGAGAGGGA 59.571 52.381 0.00 0.00 0.00 4.20
114 115 1.822371 GGACAGACAGAAGAGAGGGAC 59.178 57.143 0.00 0.00 0.00 4.46
115 116 6.880934 CTGGACAGACAGAAGAGAGGGACT 62.881 54.167 0.00 0.00 41.13 3.85
116 117 2.491693 GACAGACAGAAGAGAGGGACTG 59.508 54.545 0.00 0.00 41.55 3.51
117 118 1.824230 CAGACAGAAGAGAGGGACTGG 59.176 57.143 0.00 0.00 41.55 4.00
118 119 1.713647 AGACAGAAGAGAGGGACTGGA 59.286 52.381 0.00 0.00 41.55 3.86
119 120 2.110899 AGACAGAAGAGAGGGACTGGAA 59.889 50.000 0.00 0.00 41.55 3.53
120 121 2.232696 GACAGAAGAGAGGGACTGGAAC 59.767 54.545 0.00 0.00 41.55 3.62
121 122 1.552792 CAGAAGAGAGGGACTGGAACC 59.447 57.143 0.00 0.00 41.55 3.62
122 123 1.150135 AGAAGAGAGGGACTGGAACCA 59.850 52.381 0.00 0.00 41.55 3.67
123 124 1.978580 GAAGAGAGGGACTGGAACCAA 59.021 52.381 0.00 0.00 41.55 3.67
124 125 2.350863 AGAGAGGGACTGGAACCAAT 57.649 50.000 0.00 0.00 41.55 3.16
125 126 1.912043 AGAGAGGGACTGGAACCAATG 59.088 52.381 0.00 0.00 41.55 2.82
126 127 0.329596 AGAGGGACTGGAACCAATGC 59.670 55.000 0.00 0.00 41.55 3.56
127 128 0.681243 GAGGGACTGGAACCAATGCC 60.681 60.000 4.74 4.74 41.55 4.40
128 129 1.682344 GGGACTGGAACCAATGCCC 60.682 63.158 1.48 5.74 27.21 5.36
129 130 1.076549 GGACTGGAACCAATGCCCA 59.923 57.895 0.00 0.00 0.00 5.36
130 131 0.324645 GGACTGGAACCAATGCCCAT 60.325 55.000 0.00 0.00 0.00 4.00
131 132 0.819582 GACTGGAACCAATGCCCATG 59.180 55.000 0.00 0.00 0.00 3.66
132 133 0.615544 ACTGGAACCAATGCCCATGG 60.616 55.000 4.14 4.14 43.84 3.66
133 134 1.305971 TGGAACCAATGCCCATGGG 60.306 57.895 27.87 27.87 42.48 4.00
143 144 2.839162 CCCATGGGCGGATTTGGG 60.839 66.667 20.41 0.00 42.72 4.12
144 145 3.539791 CCATGGGCGGATTTGGGC 61.540 66.667 2.85 0.00 0.00 5.36
182 183 2.282180 GCCTGGGGCGTGAGAAAA 60.282 61.111 0.00 0.00 39.62 2.29
183 184 1.901464 GCCTGGGGCGTGAGAAAAA 60.901 57.895 0.00 0.00 39.62 1.94
184 185 1.250840 GCCTGGGGCGTGAGAAAAAT 61.251 55.000 0.00 0.00 39.62 1.82
185 186 1.256812 CCTGGGGCGTGAGAAAAATT 58.743 50.000 0.00 0.00 0.00 1.82
186 187 1.202348 CCTGGGGCGTGAGAAAAATTC 59.798 52.381 0.00 0.00 0.00 2.17
187 188 2.162681 CTGGGGCGTGAGAAAAATTCT 58.837 47.619 0.00 0.00 44.21 2.40
223 224 1.757949 AAAAATGTTTGGCCGGGGG 59.242 52.632 2.18 0.00 0.00 5.40
245 246 3.369921 GCCCAGTTTGAAGGCCAG 58.630 61.111 5.01 0.00 41.00 4.85
246 247 2.278330 GCCCAGTTTGAAGGCCAGG 61.278 63.158 5.01 0.00 41.00 4.45
247 248 2.278330 CCCAGTTTGAAGGCCAGGC 61.278 63.158 5.01 1.26 0.00 4.85
248 249 1.531365 CCAGTTTGAAGGCCAGGCA 60.531 57.895 15.19 0.00 0.00 4.75
249 250 1.530013 CCAGTTTGAAGGCCAGGCAG 61.530 60.000 15.19 0.00 0.00 4.85
250 251 1.905354 AGTTTGAAGGCCAGGCAGC 60.905 57.895 15.19 1.76 0.00 5.25
291 292 4.020617 CAGCCCAACTCCCGCAGA 62.021 66.667 0.00 0.00 0.00 4.26
292 293 4.021925 AGCCCAACTCCCGCAGAC 62.022 66.667 0.00 0.00 0.00 3.51
293 294 4.329545 GCCCAACTCCCGCAGACA 62.330 66.667 0.00 0.00 0.00 3.41
294 295 2.046892 CCCAACTCCCGCAGACAG 60.047 66.667 0.00 0.00 0.00 3.51
295 296 2.743928 CCAACTCCCGCAGACAGC 60.744 66.667 0.00 0.00 40.87 4.40
296 297 2.031012 CAACTCCCGCAGACAGCA 59.969 61.111 0.00 0.00 46.13 4.41
297 298 2.031516 CAACTCCCGCAGACAGCAG 61.032 63.158 0.00 0.00 46.13 4.24
298 299 2.210013 AACTCCCGCAGACAGCAGA 61.210 57.895 0.00 0.00 46.13 4.26
299 300 2.125753 CTCCCGCAGACAGCAGAC 60.126 66.667 0.00 0.00 46.13 3.51
300 301 2.601666 TCCCGCAGACAGCAGACT 60.602 61.111 0.00 0.00 46.13 3.24
301 302 2.125753 CCCGCAGACAGCAGACTC 60.126 66.667 0.00 0.00 46.13 3.36
302 303 2.505777 CCGCAGACAGCAGACTCG 60.506 66.667 0.00 0.00 46.13 4.18
303 304 3.177920 CGCAGACAGCAGACTCGC 61.178 66.667 0.00 0.00 46.13 5.03
304 305 2.261052 GCAGACAGCAGACTCGCT 59.739 61.111 0.00 0.00 45.21 4.93
305 306 1.805134 GCAGACAGCAGACTCGCTC 60.805 63.158 0.00 0.00 41.38 5.03
306 307 1.583477 CAGACAGCAGACTCGCTCA 59.417 57.895 0.00 0.00 41.38 4.26
307 308 0.732196 CAGACAGCAGACTCGCTCAC 60.732 60.000 0.00 0.00 41.38 3.51
308 309 1.445238 GACAGCAGACTCGCTCACC 60.445 63.158 0.00 0.00 41.38 4.02
309 310 2.505777 CAGCAGACTCGCTCACCG 60.506 66.667 0.00 0.00 41.38 4.94
310 311 4.427661 AGCAGACTCGCTCACCGC 62.428 66.667 0.00 0.00 37.91 5.68
311 312 4.724602 GCAGACTCGCTCACCGCA 62.725 66.667 0.00 0.00 39.08 5.69
312 313 2.807045 CAGACTCGCTCACCGCAC 60.807 66.667 0.00 0.00 39.08 5.34
313 314 4.406173 AGACTCGCTCACCGCACG 62.406 66.667 0.00 0.00 39.08 5.34
314 315 4.400109 GACTCGCTCACCGCACGA 62.400 66.667 0.00 0.00 39.08 4.35
315 316 3.891586 GACTCGCTCACCGCACGAA 62.892 63.158 0.00 0.00 39.08 3.85
316 317 3.470567 CTCGCTCACCGCACGAAC 61.471 66.667 0.00 0.00 39.08 3.95
319 320 3.414700 GCTCACCGCACGAACCAG 61.415 66.667 0.00 0.00 38.92 4.00
320 321 3.414700 CTCACCGCACGAACCAGC 61.415 66.667 0.00 0.00 0.00 4.85
321 322 4.980805 TCACCGCACGAACCAGCC 62.981 66.667 0.00 0.00 0.00 4.85
323 324 4.988598 ACCGCACGAACCAGCCAG 62.989 66.667 0.00 0.00 0.00 4.85
324 325 4.680237 CCGCACGAACCAGCCAGA 62.680 66.667 0.00 0.00 0.00 3.86
325 326 3.414700 CGCACGAACCAGCCAGAC 61.415 66.667 0.00 0.00 0.00 3.51
326 327 3.414700 GCACGAACCAGCCAGACG 61.415 66.667 0.00 0.00 0.00 4.18
327 328 3.414700 CACGAACCAGCCAGACGC 61.415 66.667 0.00 0.00 37.98 5.19
328 329 3.923864 ACGAACCAGCCAGACGCA 61.924 61.111 0.00 0.00 41.38 5.24
329 330 3.114616 CGAACCAGCCAGACGCAG 61.115 66.667 0.00 0.00 41.38 5.18
330 331 3.426568 GAACCAGCCAGACGCAGC 61.427 66.667 0.00 0.00 41.38 5.25
344 345 4.821589 CAGCCGCCCCGTCTCTTC 62.822 72.222 0.00 0.00 0.00 2.87
362 363 3.391382 CCCCCGACCTCACCTGAC 61.391 72.222 0.00 0.00 0.00 3.51
363 364 3.760035 CCCCGACCTCACCTGACG 61.760 72.222 0.00 0.00 0.00 4.35
364 365 2.675423 CCCGACCTCACCTGACGA 60.675 66.667 0.00 0.00 0.00 4.20
365 366 2.273179 CCCGACCTCACCTGACGAA 61.273 63.158 0.00 0.00 0.00 3.85
366 367 1.080705 CCGACCTCACCTGACGAAC 60.081 63.158 0.00 0.00 0.00 3.95
367 368 1.080705 CGACCTCACCTGACGAACC 60.081 63.158 0.00 0.00 0.00 3.62
368 369 1.292541 GACCTCACCTGACGAACCC 59.707 63.158 0.00 0.00 0.00 4.11
369 370 1.152312 ACCTCACCTGACGAACCCT 60.152 57.895 0.00 0.00 0.00 4.34
370 371 0.113776 ACCTCACCTGACGAACCCTA 59.886 55.000 0.00 0.00 0.00 3.53
371 372 1.263356 CCTCACCTGACGAACCCTAA 58.737 55.000 0.00 0.00 0.00 2.69
372 373 1.204941 CCTCACCTGACGAACCCTAAG 59.795 57.143 0.00 0.00 0.00 2.18
373 374 0.606604 TCACCTGACGAACCCTAAGC 59.393 55.000 0.00 0.00 0.00 3.09
374 375 0.608640 CACCTGACGAACCCTAAGCT 59.391 55.000 0.00 0.00 0.00 3.74
375 376 0.608640 ACCTGACGAACCCTAAGCTG 59.391 55.000 0.00 0.00 0.00 4.24
376 377 0.741221 CCTGACGAACCCTAAGCTGC 60.741 60.000 0.00 0.00 0.00 5.25
377 378 0.741221 CTGACGAACCCTAAGCTGCC 60.741 60.000 0.00 0.00 0.00 4.85
378 379 1.810030 GACGAACCCTAAGCTGCCG 60.810 63.158 0.00 0.00 0.00 5.69
379 380 3.195698 CGAACCCTAAGCTGCCGC 61.196 66.667 0.00 0.00 0.00 6.53
380 381 2.824489 GAACCCTAAGCTGCCGCC 60.824 66.667 0.00 0.00 36.60 6.13
381 382 4.778143 AACCCTAAGCTGCCGCCG 62.778 66.667 0.00 0.00 36.60 6.46
385 386 4.451150 CTAAGCTGCCGCCGGTCA 62.451 66.667 4.45 2.17 36.60 4.02
386 387 4.752879 TAAGCTGCCGCCGGTCAC 62.753 66.667 4.45 0.00 36.60 3.67
411 412 4.717629 CGTCGCCGCTCAACTCCA 62.718 66.667 0.00 0.00 0.00 3.86
412 413 2.125512 GTCGCCGCTCAACTCCAT 60.126 61.111 0.00 0.00 0.00 3.41
413 414 2.167861 GTCGCCGCTCAACTCCATC 61.168 63.158 0.00 0.00 0.00 3.51
414 415 2.185350 CGCCGCTCAACTCCATCT 59.815 61.111 0.00 0.00 0.00 2.90
415 416 2.169789 CGCCGCTCAACTCCATCTG 61.170 63.158 0.00 0.00 0.00 2.90
416 417 1.817099 GCCGCTCAACTCCATCTGG 60.817 63.158 0.00 0.00 0.00 3.86
417 418 1.817099 CCGCTCAACTCCATCTGGC 60.817 63.158 0.00 0.00 34.44 4.85
418 419 1.078918 CGCTCAACTCCATCTGGCA 60.079 57.895 0.00 0.00 34.44 4.92
419 420 1.088340 CGCTCAACTCCATCTGGCAG 61.088 60.000 8.58 8.58 34.44 4.85
420 421 0.251354 GCTCAACTCCATCTGGCAGA 59.749 55.000 21.19 21.19 34.44 4.26
421 422 1.134159 GCTCAACTCCATCTGGCAGAT 60.134 52.381 24.01 24.01 34.74 2.90
652 653 3.022981 CTCGAGTCTTCGTTCCAGC 57.977 57.895 3.62 0.00 46.72 4.85
653 654 0.794981 CTCGAGTCTTCGTTCCAGCG 60.795 60.000 3.62 0.00 46.72 5.18
654 655 2.437343 CGAGTCTTCGTTCCAGCGC 61.437 63.158 0.00 0.00 41.84 5.92
655 656 2.048127 AGTCTTCGTTCCAGCGCC 60.048 61.111 2.29 0.00 0.00 6.53
656 657 3.119096 GTCTTCGTTCCAGCGCCC 61.119 66.667 2.29 0.00 0.00 6.13
657 658 4.388499 TCTTCGTTCCAGCGCCCC 62.388 66.667 2.29 0.00 0.00 5.80
686 687 2.933834 CCCAGGAGGAACCCGGTT 60.934 66.667 1.22 1.22 40.05 4.44
687 688 2.351276 CCAGGAGGAACCCGGTTG 59.649 66.667 7.78 0.00 40.05 3.77
688 689 2.359975 CAGGAGGAACCCGGTTGC 60.360 66.667 13.71 13.71 40.05 4.17
689 690 4.016706 AGGAGGAACCCGGTTGCG 62.017 66.667 15.40 0.00 38.85 4.85
719 720 3.060615 CTTGCCTGCTGCCCTGTC 61.061 66.667 0.00 0.00 40.16 3.51
720 721 4.666253 TTGCCTGCTGCCCTGTCC 62.666 66.667 0.00 0.00 40.16 4.02
808 809 4.549516 GCGTCCGGCGAGGTAGTC 62.550 72.222 20.06 0.00 44.77 2.59
809 810 3.129502 CGTCCGGCGAGGTAGTCA 61.130 66.667 9.30 0.00 44.77 3.41
810 811 2.799371 GTCCGGCGAGGTAGTCAG 59.201 66.667 9.30 0.00 41.99 3.51
811 812 2.045131 GTCCGGCGAGGTAGTCAGT 61.045 63.158 9.30 0.00 41.99 3.41
812 813 2.044555 TCCGGCGAGGTAGTCAGTG 61.045 63.158 9.30 0.00 41.99 3.66
813 814 2.490217 CGGCGAGGTAGTCAGTGG 59.510 66.667 0.00 0.00 0.00 4.00
814 815 2.184579 GGCGAGGTAGTCAGTGGC 59.815 66.667 0.00 0.00 0.00 5.01
815 816 2.352032 GGCGAGGTAGTCAGTGGCT 61.352 63.158 1.28 1.28 0.00 4.75
816 817 1.139947 GCGAGGTAGTCAGTGGCTC 59.860 63.158 0.00 0.00 0.00 4.70
817 818 1.595993 GCGAGGTAGTCAGTGGCTCA 61.596 60.000 0.00 0.00 0.00 4.26
818 819 0.171455 CGAGGTAGTCAGTGGCTCAC 59.829 60.000 0.00 0.00 34.10 3.51
819 820 1.257743 GAGGTAGTCAGTGGCTCACA 58.742 55.000 0.00 0.00 36.74 3.58
820 821 1.203523 GAGGTAGTCAGTGGCTCACAG 59.796 57.143 0.00 0.67 36.74 3.66
821 822 0.390472 GGTAGTCAGTGGCTCACAGC 60.390 60.000 0.00 0.00 41.46 4.40
822 823 0.605589 GTAGTCAGTGGCTCACAGCT 59.394 55.000 0.00 0.00 41.99 4.24
823 824 0.891373 TAGTCAGTGGCTCACAGCTC 59.109 55.000 0.00 0.00 41.99 4.09
824 825 1.117749 AGTCAGTGGCTCACAGCTCA 61.118 55.000 0.00 0.00 41.99 4.26
825 826 0.948141 GTCAGTGGCTCACAGCTCAC 60.948 60.000 7.86 8.32 41.99 3.51
826 827 1.117749 TCAGTGGCTCACAGCTCACT 61.118 55.000 11.58 11.58 46.32 3.41
827 828 1.370437 AGTGGCTCACAGCTCACTG 59.630 57.895 14.87 0.00 44.87 3.66
837 838 2.183046 GCTCACTGCTCGGTCCTC 59.817 66.667 0.00 0.00 38.95 3.71
838 839 2.640302 GCTCACTGCTCGGTCCTCA 61.640 63.158 0.00 0.00 38.95 3.86
839 840 1.214062 CTCACTGCTCGGTCCTCAC 59.786 63.158 0.00 0.00 0.00 3.51
840 841 1.228583 TCACTGCTCGGTCCTCACT 60.229 57.895 0.00 0.00 0.00 3.41
841 842 0.827925 TCACTGCTCGGTCCTCACTT 60.828 55.000 0.00 0.00 0.00 3.16
842 843 0.888619 CACTGCTCGGTCCTCACTTA 59.111 55.000 0.00 0.00 0.00 2.24
843 844 1.135257 CACTGCTCGGTCCTCACTTAG 60.135 57.143 0.00 0.00 0.00 2.18
844 845 1.178276 CTGCTCGGTCCTCACTTAGT 58.822 55.000 0.00 0.00 0.00 2.24
845 846 1.133407 CTGCTCGGTCCTCACTTAGTC 59.867 57.143 0.00 0.00 0.00 2.59
846 847 1.174783 GCTCGGTCCTCACTTAGTCA 58.825 55.000 0.00 0.00 0.00 3.41
847 848 1.135344 GCTCGGTCCTCACTTAGTCAC 60.135 57.143 0.00 0.00 0.00 3.67
848 849 2.438411 CTCGGTCCTCACTTAGTCACT 58.562 52.381 0.00 0.00 0.00 3.41
849 850 2.820787 CTCGGTCCTCACTTAGTCACTT 59.179 50.000 0.00 0.00 0.00 3.16
850 851 3.228453 TCGGTCCTCACTTAGTCACTTT 58.772 45.455 0.00 0.00 0.00 2.66
851 852 3.255149 TCGGTCCTCACTTAGTCACTTTC 59.745 47.826 0.00 0.00 0.00 2.62
852 853 3.256136 CGGTCCTCACTTAGTCACTTTCT 59.744 47.826 0.00 0.00 0.00 2.52
853 854 4.616373 CGGTCCTCACTTAGTCACTTTCTC 60.616 50.000 0.00 0.00 0.00 2.87
854 855 4.281182 GGTCCTCACTTAGTCACTTTCTCA 59.719 45.833 0.00 0.00 0.00 3.27
855 856 5.465935 GTCCTCACTTAGTCACTTTCTCAG 58.534 45.833 0.00 0.00 0.00 3.35
856 857 4.524714 TCCTCACTTAGTCACTTTCTCAGG 59.475 45.833 0.00 0.00 0.00 3.86
857 858 4.282195 CCTCACTTAGTCACTTTCTCAGGT 59.718 45.833 0.00 0.00 0.00 4.00
858 859 5.221541 CCTCACTTAGTCACTTTCTCAGGTT 60.222 44.000 0.00 0.00 0.00 3.50
859 860 6.235231 TCACTTAGTCACTTTCTCAGGTTT 57.765 37.500 0.00 0.00 0.00 3.27
860 861 6.650120 TCACTTAGTCACTTTCTCAGGTTTT 58.350 36.000 0.00 0.00 0.00 2.43
861 862 6.538742 TCACTTAGTCACTTTCTCAGGTTTTG 59.461 38.462 0.00 0.00 0.00 2.44
862 863 6.538742 CACTTAGTCACTTTCTCAGGTTTTGA 59.461 38.462 0.00 0.00 0.00 2.69
863 864 7.227512 CACTTAGTCACTTTCTCAGGTTTTGAT 59.772 37.037 0.00 0.00 34.68 2.57
864 865 8.429641 ACTTAGTCACTTTCTCAGGTTTTGATA 58.570 33.333 0.00 0.00 34.68 2.15
865 866 8.833231 TTAGTCACTTTCTCAGGTTTTGATAG 57.167 34.615 0.00 0.00 34.68 2.08
866 867 5.703130 AGTCACTTTCTCAGGTTTTGATAGC 59.297 40.000 0.00 0.00 34.68 2.97
867 868 5.703130 GTCACTTTCTCAGGTTTTGATAGCT 59.297 40.000 0.00 0.00 34.68 3.32
868 869 6.205658 GTCACTTTCTCAGGTTTTGATAGCTT 59.794 38.462 0.00 0.00 34.68 3.74
869 870 6.205464 TCACTTTCTCAGGTTTTGATAGCTTG 59.795 38.462 0.00 0.00 34.68 4.01
870 871 6.205464 CACTTTCTCAGGTTTTGATAGCTTGA 59.795 38.462 0.00 0.00 34.68 3.02
871 872 6.944862 ACTTTCTCAGGTTTTGATAGCTTGAT 59.055 34.615 0.00 0.00 34.68 2.57
872 873 6.748333 TTCTCAGGTTTTGATAGCTTGATG 57.252 37.500 0.00 0.00 34.68 3.07
873 874 4.637534 TCTCAGGTTTTGATAGCTTGATGC 59.362 41.667 0.00 0.00 37.25 3.91
874 875 3.696051 TCAGGTTTTGATAGCTTGATGCC 59.304 43.478 0.00 0.00 44.23 4.40
875 876 3.444742 CAGGTTTTGATAGCTTGATGCCA 59.555 43.478 0.00 0.00 44.23 4.92
876 877 4.098960 CAGGTTTTGATAGCTTGATGCCAT 59.901 41.667 0.00 0.00 44.23 4.40
877 878 4.098960 AGGTTTTGATAGCTTGATGCCATG 59.901 41.667 0.00 0.00 44.23 3.66
878 879 3.720949 TTTGATAGCTTGATGCCATGC 57.279 42.857 0.00 0.00 44.23 4.06
884 885 2.088950 GCTTGATGCCATGCTTTTGT 57.911 45.000 0.00 0.00 39.52 2.83
885 886 2.419667 GCTTGATGCCATGCTTTTGTT 58.580 42.857 0.00 0.00 39.52 2.83
886 887 2.809696 GCTTGATGCCATGCTTTTGTTT 59.190 40.909 0.00 0.00 39.52 2.83
887 888 3.995705 GCTTGATGCCATGCTTTTGTTTA 59.004 39.130 0.00 0.00 39.52 2.01
888 889 4.632688 GCTTGATGCCATGCTTTTGTTTAT 59.367 37.500 0.00 0.00 39.52 1.40
889 890 5.220529 GCTTGATGCCATGCTTTTGTTTATC 60.221 40.000 0.00 0.00 39.52 1.75
926 927 3.694043 TGCTAGATGCCACTGTTTGTA 57.306 42.857 0.00 0.00 42.00 2.41
929 934 3.242870 GCTAGATGCCACTGTTTGTATGC 60.243 47.826 0.00 0.00 35.15 3.14
939 944 6.093495 GCCACTGTTTGTATGCTTGTTAGATA 59.907 38.462 0.00 0.00 0.00 1.98
948 953 8.812147 TGTATGCTTGTTAGATATAGAAACCG 57.188 34.615 0.00 0.00 0.00 4.44
949 954 8.635328 TGTATGCTTGTTAGATATAGAAACCGA 58.365 33.333 0.00 0.00 0.00 4.69
1072 3229 5.292101 CCGAAACCAACTAGACTCATTCATC 59.708 44.000 0.00 0.00 0.00 2.92
1130 3287 2.028420 TGATCTTGGTCATCTTGCCG 57.972 50.000 0.00 0.00 0.00 5.69
1214 3371 3.836949 AGCATTGATTTTACCTGTTGCG 58.163 40.909 0.00 0.00 34.20 4.85
1215 3372 2.923020 GCATTGATTTTACCTGTTGCGG 59.077 45.455 0.00 0.00 0.00 5.69
1216 3373 3.613910 GCATTGATTTTACCTGTTGCGGT 60.614 43.478 0.00 0.00 41.10 5.68
1217 3374 4.555262 CATTGATTTTACCTGTTGCGGTT 58.445 39.130 0.00 0.00 38.49 4.44
1231 3405 0.179124 GCGGTTTGCAACAGTGGAAA 60.179 50.000 0.00 0.00 42.14 3.13
1239 3413 2.294233 TGCAACAGTGGAAAGAGCATTC 59.706 45.455 0.00 0.00 0.00 2.67
1253 3427 5.946942 AGAGCATTCTCAAGACTGGATTA 57.053 39.130 0.00 0.00 41.81 1.75
1295 3469 7.754851 TGATTGGATGAATCATAGAATGGTG 57.245 36.000 0.00 0.00 44.65 4.17
1505 3686 6.109359 TGAAGGTTTAGCTTCTTCTGCTATC 58.891 40.000 19.02 0.00 41.83 2.08
1522 3703 4.827284 TGCTATCGAAGATGTAGTCATGGA 59.173 41.667 0.00 0.00 45.12 3.41
1589 3771 9.956720 TTGTATCATCGATCTATGCTACATATG 57.043 33.333 18.89 0.00 37.93 1.78
1627 3810 6.945435 TCTTGCTTTATTAGTTGACCCATCAA 59.055 34.615 0.00 0.00 42.73 2.57
1647 3830 5.049167 TCAAGGAACAAATGTTGTCATTGC 58.951 37.500 3.05 0.00 44.59 3.56
1696 3881 7.756722 AGTTATGCAACATAGATTGACTTTTGC 59.243 33.333 0.00 0.00 37.76 3.68
1846 4038 3.500680 GGCTGTTGGTTTCAGATAACGAA 59.499 43.478 0.00 0.00 35.20 3.85
1848 4040 4.213482 GCTGTTGGTTTCAGATAACGAACT 59.787 41.667 16.56 0.00 43.11 3.01
1849 4041 5.407387 GCTGTTGGTTTCAGATAACGAACTA 59.593 40.000 16.56 8.46 43.11 2.24
1850 4042 6.073440 GCTGTTGGTTTCAGATAACGAACTAA 60.073 38.462 16.56 2.50 43.11 2.24
1857 4049 8.771766 GGTTTCAGATAACGAACTAATAATCCC 58.228 37.037 0.00 0.00 0.00 3.85
1902 4094 4.075682 GGGAGAAAGAAACAAGGAGGAAG 58.924 47.826 0.00 0.00 0.00 3.46
2151 4379 3.744660 AGGCTGAGAGTTTTTGTTCGAT 58.255 40.909 0.00 0.00 0.00 3.59
2173 4401 8.512956 TCGATAAACAGAGCATATAGTCCTAAC 58.487 37.037 0.00 0.00 0.00 2.34
2210 4441 9.288124 CATAGCTCATACTTCAGAATAGAATCG 57.712 37.037 0.00 0.00 0.00 3.34
2212 4443 5.866633 GCTCATACTTCAGAATAGAATCGGG 59.133 44.000 0.00 0.00 0.00 5.14
2237 4468 3.493350 GCTGTCTTCTTCTCTGTTGGTCA 60.493 47.826 0.00 0.00 0.00 4.02
2241 4472 3.903714 TCTTCTTCTCTGTTGGTCATGGA 59.096 43.478 0.00 0.00 0.00 3.41
2330 4561 2.561478 ACCGGATAATGCGCCTAATT 57.439 45.000 9.46 0.00 0.00 1.40
2372 4603 5.250982 TCAATGGGCTGCTAATAGATGATG 58.749 41.667 0.00 0.00 0.00 3.07
2473 4704 4.832248 CAGGCACTTTATCTGACTGGTTA 58.168 43.478 0.00 0.00 40.63 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.747108 GCAAGATACACGCAGAGAATACAT 59.253 41.667 0.00 0.00 0.00 2.29
19 20 4.112634 GCAAGATACACGCAGAGAATACA 58.887 43.478 0.00 0.00 0.00 2.29
20 21 3.180584 CGCAAGATACACGCAGAGAATAC 59.819 47.826 0.00 0.00 43.02 1.89
21 22 3.372060 CGCAAGATACACGCAGAGAATA 58.628 45.455 0.00 0.00 43.02 1.75
71 72 1.429299 TCCCTCTCTTCTGTCTGTCCA 59.571 52.381 0.00 0.00 0.00 4.02
79 80 1.824230 CTGTCCAGTCCCTCTCTTCTG 59.176 57.143 0.00 0.00 0.00 3.02
84 85 1.181786 CTGTCTGTCCAGTCCCTCTC 58.818 60.000 0.00 0.00 0.00 3.20
97 98 1.824230 CCAGTCCCTCTCTTCTGTCTG 59.176 57.143 0.00 0.00 0.00 3.51
98 99 1.713647 TCCAGTCCCTCTCTTCTGTCT 59.286 52.381 0.00 0.00 0.00 3.41
99 100 2.223803 TCCAGTCCCTCTCTTCTGTC 57.776 55.000 0.00 0.00 0.00 3.51
100 101 2.252714 GTTCCAGTCCCTCTCTTCTGT 58.747 52.381 0.00 0.00 0.00 3.41
101 102 1.552792 GGTTCCAGTCCCTCTCTTCTG 59.447 57.143 0.00 0.00 0.00 3.02
102 103 1.150135 TGGTTCCAGTCCCTCTCTTCT 59.850 52.381 0.00 0.00 0.00 2.85
103 104 1.645710 TGGTTCCAGTCCCTCTCTTC 58.354 55.000 0.00 0.00 0.00 2.87
104 105 2.118403 TTGGTTCCAGTCCCTCTCTT 57.882 50.000 0.00 0.00 0.00 2.85
105 106 1.912043 CATTGGTTCCAGTCCCTCTCT 59.088 52.381 0.00 0.00 0.00 3.10
106 107 1.680249 GCATTGGTTCCAGTCCCTCTC 60.680 57.143 0.00 0.00 0.00 3.20
107 108 0.329596 GCATTGGTTCCAGTCCCTCT 59.670 55.000 0.00 0.00 0.00 3.69
108 109 0.681243 GGCATTGGTTCCAGTCCCTC 60.681 60.000 0.00 0.00 0.00 4.30
109 110 1.384191 GGCATTGGTTCCAGTCCCT 59.616 57.895 0.00 0.00 0.00 4.20
110 111 1.682344 GGGCATTGGTTCCAGTCCC 60.682 63.158 8.53 8.53 0.00 4.46
111 112 0.324645 ATGGGCATTGGTTCCAGTCC 60.325 55.000 0.00 0.00 33.68 3.85
112 113 0.819582 CATGGGCATTGGTTCCAGTC 59.180 55.000 0.00 0.00 33.68 3.51
113 114 0.615544 CCATGGGCATTGGTTCCAGT 60.616 55.000 2.85 0.00 33.68 4.00
114 115 1.332144 CCCATGGGCATTGGTTCCAG 61.332 60.000 20.41 0.00 33.68 3.86
115 116 1.305971 CCCATGGGCATTGGTTCCA 60.306 57.895 20.41 0.00 34.79 3.53
116 117 3.632896 CCCATGGGCATTGGTTCC 58.367 61.111 20.41 0.00 0.00 3.62
126 127 2.839162 CCCAAATCCGCCCATGGG 60.839 66.667 27.87 27.87 46.07 4.00
127 128 3.539791 GCCCAAATCCGCCCATGG 61.540 66.667 4.14 4.14 0.00 3.66
128 129 3.539791 GGCCCAAATCCGCCCATG 61.540 66.667 0.00 0.00 39.39 3.66
165 166 1.250840 ATTTTTCTCACGCCCCAGGC 61.251 55.000 0.00 0.00 46.75 4.85
166 167 1.202348 GAATTTTTCTCACGCCCCAGG 59.798 52.381 0.00 0.00 0.00 4.45
167 168 2.162681 AGAATTTTTCTCACGCCCCAG 58.837 47.619 0.00 0.00 34.07 4.45
168 169 2.286365 AGAATTTTTCTCACGCCCCA 57.714 45.000 0.00 0.00 34.07 4.96
205 206 1.757949 CCCCCGGCCAAACATTTTT 59.242 52.632 2.24 0.00 0.00 1.94
206 207 2.889606 GCCCCCGGCCAAACATTTT 61.890 57.895 2.24 0.00 44.06 1.82
207 208 3.318384 GCCCCCGGCCAAACATTT 61.318 61.111 2.24 0.00 44.06 2.32
223 224 1.923227 GCCTTCAAACTGGGCTACGC 61.923 60.000 0.00 0.00 42.31 4.42
224 225 1.305930 GGCCTTCAAACTGGGCTACG 61.306 60.000 0.00 0.00 44.70 3.51
225 226 2.568003 GGCCTTCAAACTGGGCTAC 58.432 57.895 0.00 0.00 44.70 3.58
229 230 2.278330 GCCTGGCCTTCAAACTGGG 61.278 63.158 7.66 0.00 0.00 4.45
230 231 1.530013 CTGCCTGGCCTTCAAACTGG 61.530 60.000 17.53 0.00 0.00 4.00
231 232 1.962144 CTGCCTGGCCTTCAAACTG 59.038 57.895 17.53 0.00 0.00 3.16
232 233 1.905354 GCTGCCTGGCCTTCAAACT 60.905 57.895 17.53 0.00 0.00 2.66
233 234 2.653115 GCTGCCTGGCCTTCAAAC 59.347 61.111 17.53 0.00 0.00 2.93
274 275 4.020617 TCTGCGGGAGTTGGGCTG 62.021 66.667 0.00 0.00 0.00 4.85
275 276 4.021925 GTCTGCGGGAGTTGGGCT 62.022 66.667 0.00 0.00 0.00 5.19
276 277 4.329545 TGTCTGCGGGAGTTGGGC 62.330 66.667 0.00 0.00 0.00 5.36
277 278 2.046892 CTGTCTGCGGGAGTTGGG 60.047 66.667 0.00 0.00 0.00 4.12
278 279 2.743928 GCTGTCTGCGGGAGTTGG 60.744 66.667 0.00 0.00 0.00 3.77
279 280 2.031012 TGCTGTCTGCGGGAGTTG 59.969 61.111 0.00 0.00 46.63 3.16
280 281 2.345244 CTGCTGTCTGCGGGAGTT 59.655 61.111 2.66 0.00 46.63 3.01
286 287 3.177920 GCGAGTCTGCTGTCTGCG 61.178 66.667 0.00 1.32 46.63 5.18
287 288 2.261052 AGCGAGTCTGCTGTCTGC 59.739 61.111 8.38 0.00 45.28 4.26
303 304 3.414700 GCTGGTTCGTGCGGTGAG 61.415 66.667 0.00 0.00 0.00 3.51
304 305 4.980805 GGCTGGTTCGTGCGGTGA 62.981 66.667 0.00 0.00 0.00 4.02
306 307 4.988598 CTGGCTGGTTCGTGCGGT 62.989 66.667 0.00 0.00 0.00 5.68
307 308 4.680237 TCTGGCTGGTTCGTGCGG 62.680 66.667 0.00 0.00 0.00 5.69
308 309 3.414700 GTCTGGCTGGTTCGTGCG 61.415 66.667 0.00 0.00 0.00 5.34
309 310 3.414700 CGTCTGGCTGGTTCGTGC 61.415 66.667 0.00 0.00 0.00 5.34
310 311 3.414700 GCGTCTGGCTGGTTCGTG 61.415 66.667 0.00 0.00 39.11 4.35
311 312 3.865929 CTGCGTCTGGCTGGTTCGT 62.866 63.158 0.00 0.00 44.05 3.85
312 313 3.114616 CTGCGTCTGGCTGGTTCG 61.115 66.667 0.00 0.00 44.05 3.95
313 314 3.426568 GCTGCGTCTGGCTGGTTC 61.427 66.667 0.00 0.00 44.05 3.62
345 346 3.391382 GTCAGGTGAGGTCGGGGG 61.391 72.222 0.00 0.00 0.00 5.40
346 347 3.760035 CGTCAGGTGAGGTCGGGG 61.760 72.222 0.00 0.00 0.00 5.73
347 348 2.273179 TTCGTCAGGTGAGGTCGGG 61.273 63.158 0.00 0.00 0.00 5.14
348 349 1.080705 GTTCGTCAGGTGAGGTCGG 60.081 63.158 0.00 0.00 0.00 4.79
349 350 1.080705 GGTTCGTCAGGTGAGGTCG 60.081 63.158 0.00 0.00 0.00 4.79
350 351 1.186267 AGGGTTCGTCAGGTGAGGTC 61.186 60.000 0.00 0.00 0.00 3.85
351 352 0.113776 TAGGGTTCGTCAGGTGAGGT 59.886 55.000 0.00 0.00 0.00 3.85
352 353 1.204941 CTTAGGGTTCGTCAGGTGAGG 59.795 57.143 0.00 0.00 0.00 3.86
353 354 1.404315 GCTTAGGGTTCGTCAGGTGAG 60.404 57.143 0.00 0.00 0.00 3.51
354 355 0.606604 GCTTAGGGTTCGTCAGGTGA 59.393 55.000 0.00 0.00 0.00 4.02
355 356 0.608640 AGCTTAGGGTTCGTCAGGTG 59.391 55.000 0.00 0.00 0.00 4.00
356 357 0.608640 CAGCTTAGGGTTCGTCAGGT 59.391 55.000 0.00 0.00 0.00 4.00
357 358 0.741221 GCAGCTTAGGGTTCGTCAGG 60.741 60.000 0.00 0.00 0.00 3.86
358 359 0.741221 GGCAGCTTAGGGTTCGTCAG 60.741 60.000 0.00 0.00 0.00 3.51
359 360 1.295423 GGCAGCTTAGGGTTCGTCA 59.705 57.895 0.00 0.00 0.00 4.35
360 361 1.810030 CGGCAGCTTAGGGTTCGTC 60.810 63.158 0.00 0.00 0.00 4.20
361 362 2.264794 CGGCAGCTTAGGGTTCGT 59.735 61.111 0.00 0.00 0.00 3.85
362 363 3.195698 GCGGCAGCTTAGGGTTCG 61.196 66.667 0.00 0.00 41.01 3.95
363 364 2.824489 GGCGGCAGCTTAGGGTTC 60.824 66.667 9.17 0.00 44.37 3.62
364 365 4.778143 CGGCGGCAGCTTAGGGTT 62.778 66.667 10.53 0.00 44.37 4.11
368 369 4.451150 TGACCGGCGGCAGCTTAG 62.451 66.667 28.71 0.00 44.37 2.18
369 370 4.752879 GTGACCGGCGGCAGCTTA 62.753 66.667 28.71 0.00 44.37 3.09
395 396 2.125512 ATGGAGTTGAGCGGCGAC 60.126 61.111 12.98 4.01 0.00 5.19
396 397 2.184322 GATGGAGTTGAGCGGCGA 59.816 61.111 12.98 0.00 0.00 5.54
397 398 2.169789 CAGATGGAGTTGAGCGGCG 61.170 63.158 0.51 0.51 0.00 6.46
398 399 1.817099 CCAGATGGAGTTGAGCGGC 60.817 63.158 0.00 0.00 37.39 6.53
399 400 1.817099 GCCAGATGGAGTTGAGCGG 60.817 63.158 2.18 0.00 37.39 5.52
400 401 1.078918 TGCCAGATGGAGTTGAGCG 60.079 57.895 2.18 0.00 37.39 5.03
401 402 0.251354 TCTGCCAGATGGAGTTGAGC 59.749 55.000 2.18 0.00 37.39 4.26
402 403 2.562635 CATCTGCCAGATGGAGTTGAG 58.437 52.381 24.14 0.00 46.34 3.02
403 404 2.704464 CATCTGCCAGATGGAGTTGA 57.296 50.000 24.14 0.00 46.34 3.18
411 412 1.148723 GCTCTGCCATCTGCCAGAT 59.851 57.895 0.08 0.08 40.16 2.90
412 413 2.588439 GCTCTGCCATCTGCCAGA 59.412 61.111 0.00 0.00 40.16 3.86
637 638 2.095252 GGCGCTGGAACGAAGACTC 61.095 63.158 7.64 0.00 34.06 3.36
638 639 2.048127 GGCGCTGGAACGAAGACT 60.048 61.111 7.64 0.00 34.06 3.24
639 640 3.119096 GGGCGCTGGAACGAAGAC 61.119 66.667 7.64 0.00 34.06 3.01
640 641 4.388499 GGGGCGCTGGAACGAAGA 62.388 66.667 7.64 0.00 34.06 2.87
671 672 2.359975 GCAACCGGGTTCCTCCTG 60.360 66.667 10.04 0.00 42.06 3.86
672 673 4.016706 CGCAACCGGGTTCCTCCT 62.017 66.667 10.04 0.00 36.25 3.69
791 792 4.549516 GACTACCTCGCCGGACGC 62.550 72.222 5.05 0.00 43.23 5.19
792 793 3.109612 CTGACTACCTCGCCGGACG 62.110 68.421 5.05 9.12 45.62 4.79
793 794 2.045131 ACTGACTACCTCGCCGGAC 61.045 63.158 5.05 0.00 36.31 4.79
794 795 2.044555 CACTGACTACCTCGCCGGA 61.045 63.158 5.05 0.00 36.31 5.14
795 796 2.490217 CACTGACTACCTCGCCGG 59.510 66.667 0.00 0.00 39.35 6.13
796 797 2.490217 CCACTGACTACCTCGCCG 59.510 66.667 0.00 0.00 0.00 6.46
797 798 2.184579 GCCACTGACTACCTCGCC 59.815 66.667 0.00 0.00 0.00 5.54
798 799 1.139947 GAGCCACTGACTACCTCGC 59.860 63.158 0.00 0.00 0.00 5.03
799 800 0.171455 GTGAGCCACTGACTACCTCG 59.829 60.000 0.00 0.00 0.00 4.63
800 801 1.203523 CTGTGAGCCACTGACTACCTC 59.796 57.143 6.83 0.00 35.76 3.85
801 802 1.261480 CTGTGAGCCACTGACTACCT 58.739 55.000 6.83 0.00 35.76 3.08
802 803 0.390472 GCTGTGAGCCACTGACTACC 60.390 60.000 13.67 0.00 35.76 3.18
803 804 0.605589 AGCTGTGAGCCACTGACTAC 59.394 55.000 13.67 0.00 43.77 2.73
804 805 0.891373 GAGCTGTGAGCCACTGACTA 59.109 55.000 13.67 0.00 43.77 2.59
805 806 1.117749 TGAGCTGTGAGCCACTGACT 61.118 55.000 13.67 10.52 43.77 3.41
806 807 0.948141 GTGAGCTGTGAGCCACTGAC 60.948 60.000 13.67 8.55 43.77 3.51
807 808 1.117749 AGTGAGCTGTGAGCCACTGA 61.118 55.000 14.86 0.00 44.87 3.41
808 809 1.370437 AGTGAGCTGTGAGCCACTG 59.630 57.895 14.86 5.50 44.87 3.66
809 810 1.370437 CAGTGAGCTGTGAGCCACT 59.630 57.895 11.59 11.59 46.32 4.00
810 811 2.323580 GCAGTGAGCTGTGAGCCAC 61.324 63.158 0.00 0.00 43.77 5.01
811 812 2.031616 GCAGTGAGCTGTGAGCCA 59.968 61.111 0.00 0.00 43.77 4.75
820 821 2.183046 GAGGACCGAGCAGTGAGC 59.817 66.667 0.00 0.00 46.19 4.26
821 822 1.214062 GTGAGGACCGAGCAGTGAG 59.786 63.158 0.00 0.00 0.00 3.51
822 823 0.827925 AAGTGAGGACCGAGCAGTGA 60.828 55.000 0.00 0.00 0.00 3.41
823 824 0.888619 TAAGTGAGGACCGAGCAGTG 59.111 55.000 0.00 0.00 0.00 3.66
824 825 1.178276 CTAAGTGAGGACCGAGCAGT 58.822 55.000 0.00 0.00 0.00 4.40
825 826 1.133407 GACTAAGTGAGGACCGAGCAG 59.867 57.143 0.00 0.00 0.00 4.24
826 827 1.174783 GACTAAGTGAGGACCGAGCA 58.825 55.000 0.00 0.00 0.00 4.26
827 828 1.135344 GTGACTAAGTGAGGACCGAGC 60.135 57.143 0.00 0.00 0.00 5.03
828 829 2.438411 AGTGACTAAGTGAGGACCGAG 58.562 52.381 0.00 0.00 0.00 4.63
829 830 2.581216 AGTGACTAAGTGAGGACCGA 57.419 50.000 0.00 0.00 0.00 4.69
830 831 3.256136 AGAAAGTGACTAAGTGAGGACCG 59.744 47.826 0.00 0.00 0.00 4.79
831 832 4.281182 TGAGAAAGTGACTAAGTGAGGACC 59.719 45.833 0.00 0.00 0.00 4.46
832 833 5.455056 TGAGAAAGTGACTAAGTGAGGAC 57.545 43.478 0.00 0.00 0.00 3.85
833 834 4.524714 CCTGAGAAAGTGACTAAGTGAGGA 59.475 45.833 0.00 0.00 0.00 3.71
834 835 4.282195 ACCTGAGAAAGTGACTAAGTGAGG 59.718 45.833 0.00 0.00 0.00 3.86
835 836 5.461032 ACCTGAGAAAGTGACTAAGTGAG 57.539 43.478 0.00 0.00 0.00 3.51
836 837 5.871396 AACCTGAGAAAGTGACTAAGTGA 57.129 39.130 0.00 0.00 0.00 3.41
837 838 6.538742 TCAAAACCTGAGAAAGTGACTAAGTG 59.461 38.462 0.00 0.00 0.00 3.16
838 839 6.650120 TCAAAACCTGAGAAAGTGACTAAGT 58.350 36.000 0.00 0.00 0.00 2.24
839 840 7.736447 ATCAAAACCTGAGAAAGTGACTAAG 57.264 36.000 0.00 0.00 37.52 2.18
840 841 7.387948 GCTATCAAAACCTGAGAAAGTGACTAA 59.612 37.037 0.00 0.00 37.52 2.24
841 842 6.874134 GCTATCAAAACCTGAGAAAGTGACTA 59.126 38.462 0.00 0.00 37.52 2.59
842 843 5.703130 GCTATCAAAACCTGAGAAAGTGACT 59.297 40.000 0.00 0.00 37.52 3.41
843 844 5.703130 AGCTATCAAAACCTGAGAAAGTGAC 59.297 40.000 0.00 0.00 37.52 3.67
844 845 5.869579 AGCTATCAAAACCTGAGAAAGTGA 58.130 37.500 0.00 0.00 37.52 3.41
845 846 6.205464 TCAAGCTATCAAAACCTGAGAAAGTG 59.795 38.462 0.00 0.00 37.52 3.16
846 847 6.299141 TCAAGCTATCAAAACCTGAGAAAGT 58.701 36.000 0.00 0.00 37.52 2.66
847 848 6.808008 TCAAGCTATCAAAACCTGAGAAAG 57.192 37.500 0.00 0.00 37.52 2.62
848 849 6.349611 GCATCAAGCTATCAAAACCTGAGAAA 60.350 38.462 0.00 0.00 41.15 2.52
849 850 5.124457 GCATCAAGCTATCAAAACCTGAGAA 59.876 40.000 0.00 0.00 41.15 2.87
850 851 4.637534 GCATCAAGCTATCAAAACCTGAGA 59.362 41.667 0.00 0.00 41.15 3.27
851 852 4.201990 GGCATCAAGCTATCAAAACCTGAG 60.202 45.833 0.00 0.00 44.79 3.35
852 853 3.696051 GGCATCAAGCTATCAAAACCTGA 59.304 43.478 0.00 0.00 44.79 3.86
853 854 3.444742 TGGCATCAAGCTATCAAAACCTG 59.555 43.478 0.00 0.00 44.79 4.00
854 855 3.700538 TGGCATCAAGCTATCAAAACCT 58.299 40.909 0.00 0.00 44.79 3.50
855 856 4.365723 CATGGCATCAAGCTATCAAAACC 58.634 43.478 0.00 0.00 43.24 3.27
856 857 3.800506 GCATGGCATCAAGCTATCAAAAC 59.199 43.478 0.00 0.00 43.24 2.43
857 858 3.702548 AGCATGGCATCAAGCTATCAAAA 59.297 39.130 8.86 0.00 44.84 2.44
858 859 3.293337 AGCATGGCATCAAGCTATCAAA 58.707 40.909 8.86 0.00 44.84 2.69
859 860 2.940158 AGCATGGCATCAAGCTATCAA 58.060 42.857 8.86 0.00 44.84 2.57
860 861 2.651382 AGCATGGCATCAAGCTATCA 57.349 45.000 8.86 0.00 44.84 2.15
861 862 4.049186 CAAAAGCATGGCATCAAGCTATC 58.951 43.478 10.75 0.00 45.78 2.08
862 863 3.449737 ACAAAAGCATGGCATCAAGCTAT 59.550 39.130 10.75 1.89 45.78 2.97
863 864 2.827322 ACAAAAGCATGGCATCAAGCTA 59.173 40.909 10.75 0.00 45.78 3.32
865 866 2.088950 ACAAAAGCATGGCATCAAGC 57.911 45.000 0.00 0.00 44.65 4.01
866 867 6.035650 CAGATAAACAAAAGCATGGCATCAAG 59.964 38.462 0.00 0.00 0.00 3.02
867 868 5.870433 CAGATAAACAAAAGCATGGCATCAA 59.130 36.000 0.00 0.00 0.00 2.57
868 869 5.185442 TCAGATAAACAAAAGCATGGCATCA 59.815 36.000 0.00 0.00 0.00 3.07
869 870 5.653507 TCAGATAAACAAAAGCATGGCATC 58.346 37.500 0.00 0.00 0.00 3.91
870 871 5.664294 TCAGATAAACAAAAGCATGGCAT 57.336 34.783 0.00 0.00 0.00 4.40
871 872 5.185442 TCATCAGATAAACAAAAGCATGGCA 59.815 36.000 0.00 0.00 0.00 4.92
872 873 5.653507 TCATCAGATAAACAAAAGCATGGC 58.346 37.500 0.00 0.00 0.00 4.40
873 874 7.485810 TCATCATCAGATAAACAAAAGCATGG 58.514 34.615 0.00 0.00 31.88 3.66
874 875 9.529325 AATCATCATCAGATAAACAAAAGCATG 57.471 29.630 0.00 0.00 31.88 4.06
876 877 9.932207 AAAATCATCATCAGATAAACAAAAGCA 57.068 25.926 0.00 0.00 31.88 3.91
888 889 9.654663 CATCTAGCATCTAAAATCATCATCAGA 57.345 33.333 0.00 0.00 0.00 3.27
889 890 8.391859 GCATCTAGCATCTAAAATCATCATCAG 58.608 37.037 0.00 0.00 44.79 2.90
926 927 9.561069 AAATCGGTTTCTATATCTAACAAGCAT 57.439 29.630 0.00 0.00 0.00 3.79
939 944 9.613428 TGTCTCAATATCAAAATCGGTTTCTAT 57.387 29.630 0.00 0.00 0.00 1.98
1041 1047 1.796459 CTAGTTGGTTTCGGTGGTTCG 59.204 52.381 0.00 0.00 0.00 3.95
1072 3229 0.462759 GATCACCTCTTGCTTCCCGG 60.463 60.000 0.00 0.00 0.00 5.73
1130 3287 9.450807 GTGCATATCACTTTTAACCATATTCAC 57.549 33.333 0.00 0.00 42.38 3.18
1167 3324 3.118334 TCAACAAGACGGTAAACCAAGGA 60.118 43.478 0.00 0.00 35.14 3.36
1216 3373 2.098614 TGCTCTTTCCACTGTTGCAAA 58.901 42.857 0.00 0.00 0.00 3.68
1217 3374 1.761449 TGCTCTTTCCACTGTTGCAA 58.239 45.000 0.00 0.00 0.00 4.08
1228 3402 4.573900 TCCAGTCTTGAGAATGCTCTTTC 58.426 43.478 1.43 0.00 41.84 2.62
1231 3405 4.840716 AATCCAGTCTTGAGAATGCTCT 57.159 40.909 1.43 0.00 41.84 4.09
1239 3413 7.510549 TTTTGTTCCTTAATCCAGTCTTGAG 57.489 36.000 0.00 0.00 0.00 3.02
1253 3427 5.280113 CCAATCATCACCCATTTTGTTCCTT 60.280 40.000 0.00 0.00 0.00 3.36
1295 3469 6.589830 AATACATCTCGCTCAATGTAACAC 57.410 37.500 6.16 0.00 40.64 3.32
1475 3656 7.576477 GCAGAAGAAGCTAAACCTTCAATCATT 60.576 37.037 15.67 0.00 42.84 2.57
1505 3686 3.126831 GCCTTCCATGACTACATCTTCG 58.873 50.000 0.00 0.00 34.15 3.79
1522 3703 2.579860 AGGATTGGTTGATCTGAGCCTT 59.420 45.455 0.00 0.00 0.00 4.35
1573 3755 9.664332 AATCAAAGACCATATGTAGCATAGATC 57.336 33.333 1.24 0.00 0.00 2.75
1589 3771 9.346725 CTAATAAAGCAAGACAAATCAAAGACC 57.653 33.333 0.00 0.00 0.00 3.85
1627 3810 4.669206 TGCAATGACAACATTTGTTCCT 57.331 36.364 0.00 0.00 45.52 3.36
1846 4038 3.323979 ACGCTCATTCCGGGATTATTAGT 59.676 43.478 0.00 0.00 0.00 2.24
1848 4040 3.070446 ACACGCTCATTCCGGGATTATTA 59.930 43.478 0.00 0.00 32.49 0.98
1849 4041 2.158813 ACACGCTCATTCCGGGATTATT 60.159 45.455 0.00 0.00 32.49 1.40
1850 4042 1.416401 ACACGCTCATTCCGGGATTAT 59.584 47.619 0.00 0.00 32.49 1.28
1857 4049 0.871722 TTTTGGACACGCTCATTCCG 59.128 50.000 0.00 0.00 31.38 4.30
1902 4094 0.607489 CATAGGCCCATAGCTGTGGC 60.607 60.000 23.35 17.74 44.59 5.01
2013 4207 2.662866 CAGGGCATCAATTGTGGATCT 58.337 47.619 5.13 0.00 0.00 2.75
2016 4211 0.703488 TCCAGGGCATCAATTGTGGA 59.297 50.000 8.68 8.68 0.00 4.02
2023 4218 2.425143 GAACTCATCCAGGGCATCAA 57.575 50.000 0.00 0.00 0.00 2.57
2056 4251 7.775053 AAGATTAAGCCACATTTCCACTAAA 57.225 32.000 0.00 0.00 0.00 1.85
2151 4379 8.781196 CGTAGTTAGGACTATATGCTCTGTTTA 58.219 37.037 0.00 0.00 40.33 2.01
2166 4394 6.562518 AGCTATGAAAGTTCGTAGTTAGGAC 58.437 40.000 17.49 4.54 44.71 3.85
2173 4401 7.915923 TGAAGTATGAGCTATGAAAGTTCGTAG 59.084 37.037 13.68 13.68 45.34 3.51
2210 4441 2.829120 ACAGAGAAGAAGACAGCTACCC 59.171 50.000 0.00 0.00 0.00 3.69
2212 4443 4.241681 CCAACAGAGAAGAAGACAGCTAC 58.758 47.826 0.00 0.00 0.00 3.58
2330 4561 6.071784 CCATTGAAAAGGTCATGATGAACTGA 60.072 38.462 14.62 0.00 45.11 3.41
2372 4603 0.883833 CCTCAACTTGACCATGCACC 59.116 55.000 0.00 0.00 0.00 5.01
2443 4674 3.048600 AGATAAAGTGCCTGCCCATCTA 58.951 45.455 0.00 0.00 0.00 1.98
2473 4704 8.143193 TGTCAATTTTTCTGTATTTGAGTGCAT 58.857 29.630 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.