Multiple sequence alignment - TraesCS3A01G060400

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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 TraesCS3A01G060400 chr3A 100.000 3083 0 0 1 3083 36318472 36315390 0.000000e+00 5694.0
1 TraesCS3A01G060400 chr3A 79.839 248 49 1 1782 2028 36381803 36381556 2.440000e-41 180.0
2 TraesCS3A01G060400 chr3A 79.839 248 49 1 1782 2028 36397428 36397181 2.440000e-41 180.0
3 TraesCS3A01G060400 chr3B 92.063 1323 81 12 944 2249 44254702 44256017 0.000000e+00 1840.0
4 TraesCS3A01G060400 chr3B 90.075 534 43 5 203 729 44253824 44254354 0.000000e+00 684.0
5 TraesCS3A01G060400 chr3B 77.037 810 142 28 942 1720 44202659 44203455 2.840000e-115 425.0
6 TraesCS3A01G060400 chr3B 94.667 75 3 1 725 798 44254451 44254525 6.990000e-22 115.0
7 TraesCS3A01G060400 chr3B 90.909 66 3 2 863 925 44254562 44254627 5.480000e-13 86.1
8 TraesCS3A01G060400 chr3D 92.436 1137 70 10 1124 2249 26314540 26313409 0.000000e+00 1609.0
9 TraesCS3A01G060400 chr3D 94.153 838 45 4 2248 3083 583586486 583585651 0.000000e+00 1273.0
10 TraesCS3A01G060400 chr3D 76.326 811 148 27 942 1721 26324791 26323994 8.010000e-106 394.0
11 TraesCS3A01G060400 chr3D 84.354 147 11 5 662 798 26322068 26321924 1.930000e-27 134.0
12 TraesCS3A01G060400 chr7A 94.624 837 43 2 2248 3083 14668341 14667506 0.000000e+00 1295.0
13 TraesCS3A01G060400 chr7A 89.474 57 6 0 1584 1640 28414716 28414660 4.260000e-09 73.1
14 TraesCS3A01G060400 chr7A 91.304 46 0 4 409 451 678120619 678120575 3.320000e-05 60.2
15 TraesCS3A01G060400 chr1A 94.391 838 45 2 2246 3083 482775779 482776614 0.000000e+00 1286.0
16 TraesCS3A01G060400 chr1A 87.940 199 22 2 1 198 29095270 29095467 1.850000e-57 233.0
17 TraesCS3A01G060400 chr6A 94.385 837 45 2 2247 3083 77787205 77788039 0.000000e+00 1284.0
18 TraesCS3A01G060400 chr2B 94.251 835 45 3 2250 3083 117072603 117071771 0.000000e+00 1273.0
19 TraesCS3A01G060400 chr2B 93.817 841 49 3 2243 3083 256324899 256325736 0.000000e+00 1262.0
20 TraesCS3A01G060400 chr2B 87.923 207 20 4 1 202 550690151 550690357 3.970000e-59 239.0
21 TraesCS3A01G060400 chr2B 82.812 128 16 5 359 483 654435792 654435668 3.250000e-20 110.0
22 TraesCS3A01G060400 chr2B 81.897 116 15 5 359 469 654550826 654550712 3.270000e-15 93.5
23 TraesCS3A01G060400 chr7D 94.033 838 48 2 2246 3083 567651584 567652419 0.000000e+00 1269.0
24 TraesCS3A01G060400 chr5D 94.019 836 50 0 2248 3083 128585706 128586541 0.000000e+00 1267.0
25 TraesCS3A01G060400 chr5D 88.000 200 21 3 1 198 435192304 435192502 1.850000e-57 233.0
26 TraesCS3A01G060400 chr5D 86.634 202 23 4 1 200 41603636 41603437 1.440000e-53 220.0
27 TraesCS3A01G060400 chr2A 93.452 840 53 2 2245 3083 3396515 3395677 0.000000e+00 1245.0
28 TraesCS3A01G060400 chr2A 85.238 210 26 3 1 206 189816021 189815813 8.660000e-51 211.0
29 TraesCS3A01G060400 chr5B 92.093 215 16 1 258 471 61894200 61893986 5.000000e-78 302.0
30 TraesCS3A01G060400 chr5B 85.149 202 28 2 1 201 36236282 36236082 4.030000e-49 206.0
31 TraesCS3A01G060400 chr1D 86.730 211 24 4 1 208 324408081 324408290 6.650000e-57 231.0
32 TraesCS3A01G060400 chr1D 85.600 125 13 5 352 472 213725674 213725551 3.230000e-25 126.0
33 TraesCS3A01G060400 chrUn 87.437 199 21 3 1 198 110998820 110999015 3.090000e-55 226.0
34 TraesCS3A01G060400 chrUn 88.235 51 6 0 1568 1618 87052132 87052082 9.230000e-06 62.1
35 TraesCS3A01G060400 chr1B 86.500 200 25 2 1 198 119690821 119691020 5.180000e-53 219.0
36 TraesCS3A01G060400 chr1B 81.600 125 18 5 352 472 306701810 306701933 7.040000e-17 99.0
37 TraesCS3A01G060400 chr1B 81.897 116 17 4 352 464 306885914 306886028 9.100000e-16 95.3
38 TraesCS3A01G060400 chr2D 93.478 46 1 2 424 468 643674077 643674121 1.980000e-07 67.6


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 TraesCS3A01G060400 chr3A 36315390 36318472 3082 True 5694.000 5694 100.0000 1 3083 1 chr3A.!!$R1 3082
1 TraesCS3A01G060400 chr3B 44253824 44256017 2193 False 681.275 1840 91.9285 203 2249 4 chr3B.!!$F2 2046
2 TraesCS3A01G060400 chr3B 44202659 44203455 796 False 425.000 425 77.0370 942 1720 1 chr3B.!!$F1 778
3 TraesCS3A01G060400 chr3D 26313409 26314540 1131 True 1609.000 1609 92.4360 1124 2249 1 chr3D.!!$R1 1125
4 TraesCS3A01G060400 chr3D 583585651 583586486 835 True 1273.000 1273 94.1530 2248 3083 1 chr3D.!!$R2 835
5 TraesCS3A01G060400 chr3D 26321924 26324791 2867 True 264.000 394 80.3400 662 1721 2 chr3D.!!$R3 1059
6 TraesCS3A01G060400 chr7A 14667506 14668341 835 True 1295.000 1295 94.6240 2248 3083 1 chr7A.!!$R1 835
7 TraesCS3A01G060400 chr1A 482775779 482776614 835 False 1286.000 1286 94.3910 2246 3083 1 chr1A.!!$F2 837
8 TraesCS3A01G060400 chr6A 77787205 77788039 834 False 1284.000 1284 94.3850 2247 3083 1 chr6A.!!$F1 836
9 TraesCS3A01G060400 chr2B 117071771 117072603 832 True 1273.000 1273 94.2510 2250 3083 1 chr2B.!!$R1 833
10 TraesCS3A01G060400 chr2B 256324899 256325736 837 False 1262.000 1262 93.8170 2243 3083 1 chr2B.!!$F1 840
11 TraesCS3A01G060400 chr7D 567651584 567652419 835 False 1269.000 1269 94.0330 2246 3083 1 chr7D.!!$F1 837
12 TraesCS3A01G060400 chr5D 128585706 128586541 835 False 1267.000 1267 94.0190 2248 3083 1 chr5D.!!$F1 835
13 TraesCS3A01G060400 chr2A 3395677 3396515 838 True 1245.000 1245 93.4520 2245 3083 1 chr2A.!!$R1 838

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
300 301 0.036306 ACGCCCTGGTTTCGAAATCT 59.964 50.0 21.13 0.0 0.00 2.40 F
387 388 0.250727 GTGTTGTAGCCCCAGCAGAA 60.251 55.0 0.00 0.0 43.56 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2223 0.749454 GCTCAAATCCATCGGTGGCT 60.749 55.000 10.80 0.0 45.63 4.75 R
2299 2877 1.215382 CAGTGAACGGCGATCCAGA 59.785 57.895 16.62 0.0 0.00 3.86 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
26 27 6.817765 TGATTTACAGACCCTGAATTTGTC 57.182 37.500 0.45 0.00 35.18 3.18
27 28 6.542821 TGATTTACAGACCCTGAATTTGTCT 58.457 36.000 0.45 0.00 39.86 3.41
28 29 7.004086 TGATTTACAGACCCTGAATTTGTCTT 58.996 34.615 0.45 0.00 37.25 3.01
29 30 7.505585 TGATTTACAGACCCTGAATTTGTCTTT 59.494 33.333 0.45 0.00 37.25 2.52
30 31 7.654022 TTTACAGACCCTGAATTTGTCTTTT 57.346 32.000 0.45 0.00 37.25 2.27
31 32 7.654022 TTACAGACCCTGAATTTGTCTTTTT 57.346 32.000 0.45 0.00 37.25 1.94
32 33 5.906073 ACAGACCCTGAATTTGTCTTTTTG 58.094 37.500 0.45 0.00 37.25 2.44
33 34 4.746611 CAGACCCTGAATTTGTCTTTTTGC 59.253 41.667 0.00 0.00 37.25 3.68
34 35 4.058124 GACCCTGAATTTGTCTTTTTGCC 58.942 43.478 0.00 0.00 0.00 4.52
35 36 3.454082 ACCCTGAATTTGTCTTTTTGCCA 59.546 39.130 0.00 0.00 0.00 4.92
36 37 4.080638 ACCCTGAATTTGTCTTTTTGCCAA 60.081 37.500 0.00 0.00 0.00 4.52
37 38 4.512571 CCCTGAATTTGTCTTTTTGCCAAG 59.487 41.667 0.00 0.00 0.00 3.61
38 39 5.358922 CCTGAATTTGTCTTTTTGCCAAGA 58.641 37.500 0.00 0.00 0.00 3.02
39 40 5.464389 CCTGAATTTGTCTTTTTGCCAAGAG 59.536 40.000 0.00 0.00 33.29 2.85
40 41 5.976458 TGAATTTGTCTTTTTGCCAAGAGT 58.024 33.333 0.00 0.00 33.29 3.24
41 42 6.405538 TGAATTTGTCTTTTTGCCAAGAGTT 58.594 32.000 0.00 0.00 33.29 3.01
42 43 6.878389 TGAATTTGTCTTTTTGCCAAGAGTTT 59.122 30.769 0.00 0.00 33.29 2.66
43 44 6.908870 ATTTGTCTTTTTGCCAAGAGTTTC 57.091 33.333 0.00 0.00 33.29 2.78
44 45 5.659440 TTGTCTTTTTGCCAAGAGTTTCT 57.341 34.783 0.00 0.00 33.29 2.52
45 46 5.248870 TGTCTTTTTGCCAAGAGTTTCTC 57.751 39.130 0.00 0.00 33.29 2.87
46 47 4.704540 TGTCTTTTTGCCAAGAGTTTCTCA 59.295 37.500 0.00 0.00 33.29 3.27
47 48 5.163622 TGTCTTTTTGCCAAGAGTTTCTCAG 60.164 40.000 0.00 0.00 33.29 3.35
48 49 4.949856 TCTTTTTGCCAAGAGTTTCTCAGT 59.050 37.500 0.00 0.00 32.06 3.41
49 50 5.418840 TCTTTTTGCCAAGAGTTTCTCAGTT 59.581 36.000 0.00 0.00 32.06 3.16
50 51 4.637483 TTTGCCAAGAGTTTCTCAGTTG 57.363 40.909 0.00 0.00 32.06 3.16
51 52 3.281727 TGCCAAGAGTTTCTCAGTTGT 57.718 42.857 0.00 0.00 32.06 3.32
52 53 3.206150 TGCCAAGAGTTTCTCAGTTGTC 58.794 45.455 0.00 0.00 32.06 3.18
53 54 2.550180 GCCAAGAGTTTCTCAGTTGTCC 59.450 50.000 0.00 0.00 32.06 4.02
54 55 3.808728 CCAAGAGTTTCTCAGTTGTCCA 58.191 45.455 0.00 0.00 32.06 4.02
55 56 4.199310 CCAAGAGTTTCTCAGTTGTCCAA 58.801 43.478 0.00 0.00 32.06 3.53
56 57 4.640201 CCAAGAGTTTCTCAGTTGTCCAAA 59.360 41.667 0.00 0.00 32.06 3.28
57 58 5.300286 CCAAGAGTTTCTCAGTTGTCCAAAT 59.700 40.000 0.00 0.00 32.06 2.32
58 59 6.204359 CAAGAGTTTCTCAGTTGTCCAAATG 58.796 40.000 1.25 1.25 37.70 2.32
59 60 5.684704 AGAGTTTCTCAGTTGTCCAAATGA 58.315 37.500 9.49 9.49 42.21 2.57
60 61 6.302269 AGAGTTTCTCAGTTGTCCAAATGAT 58.698 36.000 10.20 0.00 43.23 2.45
61 62 6.774656 AGAGTTTCTCAGTTGTCCAAATGATT 59.225 34.615 10.20 0.00 43.23 2.57
62 63 7.286316 AGAGTTTCTCAGTTGTCCAAATGATTT 59.714 33.333 10.20 0.00 43.23 2.17
63 64 7.205297 AGTTTCTCAGTTGTCCAAATGATTTG 58.795 34.615 10.84 10.84 43.23 2.32
64 65 6.957920 TTCTCAGTTGTCCAAATGATTTGA 57.042 33.333 18.82 3.09 43.23 2.69
65 66 6.957920 TCTCAGTTGTCCAAATGATTTGAA 57.042 33.333 18.82 0.00 43.23 2.69
66 67 7.345422 TCTCAGTTGTCCAAATGATTTGAAA 57.655 32.000 18.82 7.78 43.23 2.69
67 68 7.780064 TCTCAGTTGTCCAAATGATTTGAAAA 58.220 30.769 18.82 7.46 43.23 2.29
68 69 8.423349 TCTCAGTTGTCCAAATGATTTGAAAAT 58.577 29.630 18.82 7.16 43.23 1.82
69 70 8.961294 TCAGTTGTCCAAATGATTTGAAAATT 57.039 26.923 18.82 4.83 40.00 1.82
72 73 9.492973 AGTTGTCCAAATGATTTGAAAATTAGG 57.507 29.630 18.82 0.18 43.26 2.69
73 74 8.720562 GTTGTCCAAATGATTTGAAAATTAGGG 58.279 33.333 18.82 0.00 43.26 3.53
74 75 6.878389 TGTCCAAATGATTTGAAAATTAGGGC 59.122 34.615 18.82 2.19 43.26 5.19
75 76 6.035975 GTCCAAATGATTTGAAAATTAGGGCG 59.964 38.462 18.82 0.00 43.26 6.13
76 77 5.294060 CCAAATGATTTGAAAATTAGGGCGG 59.706 40.000 18.82 0.00 43.26 6.13
77 78 5.930837 AATGATTTGAAAATTAGGGCGGA 57.069 34.783 0.00 0.00 0.00 5.54
78 79 4.712122 TGATTTGAAAATTAGGGCGGAC 57.288 40.909 0.00 0.00 0.00 4.79
79 80 3.445805 TGATTTGAAAATTAGGGCGGACC 59.554 43.478 0.00 0.00 40.67 4.46
91 92 2.813474 CGGACCTCGCGCATCAAA 60.813 61.111 8.75 0.00 0.00 2.69
92 93 2.173669 CGGACCTCGCGCATCAAAT 61.174 57.895 8.75 0.00 0.00 2.32
93 94 1.705337 CGGACCTCGCGCATCAAATT 61.705 55.000 8.75 0.00 0.00 1.82
94 95 0.248215 GGACCTCGCGCATCAAATTG 60.248 55.000 8.75 0.00 0.00 2.32
95 96 0.447801 GACCTCGCGCATCAAATTGT 59.552 50.000 8.75 0.00 0.00 2.71
96 97 0.447801 ACCTCGCGCATCAAATTGTC 59.552 50.000 8.75 0.00 0.00 3.18
97 98 0.729116 CCTCGCGCATCAAATTGTCT 59.271 50.000 8.75 0.00 0.00 3.41
98 99 1.933181 CCTCGCGCATCAAATTGTCTA 59.067 47.619 8.75 0.00 0.00 2.59
99 100 2.285834 CCTCGCGCATCAAATTGTCTAC 60.286 50.000 8.75 0.00 0.00 2.59
100 101 1.663643 TCGCGCATCAAATTGTCTACC 59.336 47.619 8.75 0.00 0.00 3.18
101 102 1.592110 CGCGCATCAAATTGTCTACCG 60.592 52.381 8.75 0.00 0.00 4.02
102 103 1.396996 GCGCATCAAATTGTCTACCGT 59.603 47.619 0.30 0.00 0.00 4.83
103 104 2.787723 GCGCATCAAATTGTCTACCGTG 60.788 50.000 0.30 0.00 0.00 4.94
104 105 2.223021 CGCATCAAATTGTCTACCGTGG 60.223 50.000 0.00 0.00 0.00 4.94
105 106 2.097466 GCATCAAATTGTCTACCGTGGG 59.903 50.000 0.00 0.00 0.00 4.61
106 107 3.605634 CATCAAATTGTCTACCGTGGGA 58.394 45.455 0.00 0.00 0.00 4.37
107 108 3.773418 TCAAATTGTCTACCGTGGGAA 57.227 42.857 0.00 0.00 0.00 3.97
108 109 4.088056 TCAAATTGTCTACCGTGGGAAA 57.912 40.909 0.00 0.00 0.00 3.13
109 110 4.462133 TCAAATTGTCTACCGTGGGAAAA 58.538 39.130 0.00 0.00 0.00 2.29
110 111 4.888239 TCAAATTGTCTACCGTGGGAAAAA 59.112 37.500 0.00 0.00 0.00 1.94
177 178 7.539712 TTACTTAACACAGATGCAGATAAGC 57.460 36.000 0.00 0.00 0.00 3.09
178 179 4.878397 ACTTAACACAGATGCAGATAAGCC 59.122 41.667 0.00 0.00 0.00 4.35
179 180 2.338577 ACACAGATGCAGATAAGCCC 57.661 50.000 0.00 0.00 0.00 5.19
180 181 1.224075 CACAGATGCAGATAAGCCCG 58.776 55.000 0.00 0.00 0.00 6.13
181 182 0.107456 ACAGATGCAGATAAGCCCGG 59.893 55.000 0.00 0.00 0.00 5.73
182 183 0.394192 CAGATGCAGATAAGCCCGGA 59.606 55.000 0.73 0.00 0.00 5.14
183 184 0.394565 AGATGCAGATAAGCCCGGAC 59.605 55.000 0.73 0.00 0.00 4.79
184 185 0.394565 GATGCAGATAAGCCCGGACT 59.605 55.000 0.73 0.00 0.00 3.85
185 186 0.394565 ATGCAGATAAGCCCGGACTC 59.605 55.000 0.73 0.00 0.00 3.36
186 187 0.975556 TGCAGATAAGCCCGGACTCA 60.976 55.000 0.73 0.00 0.00 3.41
187 188 0.249657 GCAGATAAGCCCGGACTCAG 60.250 60.000 0.73 0.00 0.00 3.35
188 189 1.403814 CAGATAAGCCCGGACTCAGA 58.596 55.000 0.73 0.00 0.00 3.27
189 190 1.757118 CAGATAAGCCCGGACTCAGAA 59.243 52.381 0.73 0.00 0.00 3.02
190 191 2.168521 CAGATAAGCCCGGACTCAGAAA 59.831 50.000 0.73 0.00 0.00 2.52
191 192 2.838202 AGATAAGCCCGGACTCAGAAAA 59.162 45.455 0.73 0.00 0.00 2.29
192 193 2.762535 TAAGCCCGGACTCAGAAAAG 57.237 50.000 0.73 0.00 0.00 2.27
193 194 0.036875 AAGCCCGGACTCAGAAAAGG 59.963 55.000 0.73 0.00 0.00 3.11
194 195 0.836400 AGCCCGGACTCAGAAAAGGA 60.836 55.000 0.73 0.00 0.00 3.36
195 196 0.253327 GCCCGGACTCAGAAAAGGAT 59.747 55.000 0.73 0.00 0.00 3.24
196 197 1.340114 GCCCGGACTCAGAAAAGGATT 60.340 52.381 0.73 0.00 0.00 3.01
197 198 2.880167 GCCCGGACTCAGAAAAGGATTT 60.880 50.000 0.73 0.00 42.41 2.17
198 199 3.010420 CCCGGACTCAGAAAAGGATTTC 58.990 50.000 0.73 0.00 44.34 2.17
218 219 9.320352 GGATTTCTCATAGTTTTACCTCTTCTC 57.680 37.037 0.00 0.00 0.00 2.87
221 222 5.007385 TCATAGTTTTACCTCTTCTCGGC 57.993 43.478 0.00 0.00 0.00 5.54
237 238 3.126831 CTCGGCCTGATATGAGTGAAAC 58.873 50.000 0.00 0.00 0.00 2.78
294 295 1.281656 GTCAAACGCCCTGGTTTCG 59.718 57.895 0.00 0.00 38.01 3.46
300 301 0.036306 ACGCCCTGGTTTCGAAATCT 59.964 50.000 21.13 0.00 0.00 2.40
308 309 2.736721 TGGTTTCGAAATCTCGCTGAAG 59.263 45.455 21.13 0.00 45.04 3.02
328 329 1.288127 GCACCTGGTACGAACGACT 59.712 57.895 0.00 0.00 0.00 4.18
333 334 3.374988 CACCTGGTACGAACGACTATACA 59.625 47.826 0.00 0.00 0.00 2.29
345 346 3.049912 CGACTATACAAGCGCTTGCATA 58.950 45.455 41.96 36.16 44.03 3.14
353 354 1.876322 AGCGCTTGCATATCTCCTTC 58.124 50.000 2.64 0.00 42.66 3.46
375 376 2.158740 TGTAGGGCTTGCTTGTGTTGTA 60.159 45.455 0.00 0.00 0.00 2.41
385 386 0.537143 TTGTGTTGTAGCCCCAGCAG 60.537 55.000 0.00 0.00 43.56 4.24
387 388 0.250727 GTGTTGTAGCCCCAGCAGAA 60.251 55.000 0.00 0.00 43.56 3.02
410 411 2.008329 TGTGTGTCGGTTTGTTGGTAC 58.992 47.619 0.00 0.00 0.00 3.34
412 413 2.679336 GTGTGTCGGTTTGTTGGTACTT 59.321 45.455 0.00 0.00 0.00 2.24
413 414 3.127376 GTGTGTCGGTTTGTTGGTACTTT 59.873 43.478 0.00 0.00 0.00 2.66
418 419 4.794762 GTCGGTTTGTTGGTACTTTTTGTC 59.205 41.667 0.00 0.00 0.00 3.18
423 424 3.876341 TGTTGGTACTTTTTGTCGGACT 58.124 40.909 9.88 0.00 0.00 3.85
460 462 5.347620 TTTATAAAGCAGGGCGAAGTCTA 57.652 39.130 0.00 0.00 0.00 2.59
480 483 6.144080 AGTCTATTTCGAGAAACAGTGAAACG 59.856 38.462 0.00 0.00 35.77 3.60
504 507 6.473455 CGCACAAAATTATCATTTCTCCTTCC 59.527 38.462 0.00 0.00 30.80 3.46
505 508 6.473455 GCACAAAATTATCATTTCTCCTTCCG 59.527 38.462 0.00 0.00 30.80 4.30
626 634 7.352719 AGTTGACTCTACAAATTCGTTCATC 57.647 36.000 0.00 0.00 0.00 2.92
627 635 6.369065 AGTTGACTCTACAAATTCGTTCATCC 59.631 38.462 0.00 0.00 0.00 3.51
628 636 4.862574 TGACTCTACAAATTCGTTCATCCG 59.137 41.667 0.00 0.00 0.00 4.18
631 639 4.562082 TCTACAAATTCGTTCATCCGTGT 58.438 39.130 0.00 0.00 0.00 4.49
638 646 3.692791 TCGTTCATCCGTGTATCTGAG 57.307 47.619 0.00 0.00 0.00 3.35
654 662 1.795286 CTGAGAAATATCGGCCGCTTC 59.205 52.381 23.51 19.01 0.00 3.86
666 674 2.031191 CGGCCGCTTCGTAATAATTTGT 59.969 45.455 14.67 0.00 0.00 2.83
667 675 3.486209 CGGCCGCTTCGTAATAATTTGTT 60.486 43.478 14.67 0.00 0.00 2.83
722 730 0.473755 TCTATGCATGGTGGGCGATT 59.526 50.000 10.16 0.00 0.00 3.34
760 869 4.806342 TTTTAGAGTCCAGAAACGCAAC 57.194 40.909 0.00 0.00 0.00 4.17
798 908 5.192927 TGTAGCCCAAGTCATCCTAATTTG 58.807 41.667 0.00 0.00 0.00 2.32
799 909 3.026694 AGCCCAAGTCATCCTAATTTGC 58.973 45.455 0.00 0.00 0.00 3.68
800 910 3.026694 GCCCAAGTCATCCTAATTTGCT 58.973 45.455 0.00 0.00 0.00 3.91
801 911 3.067320 GCCCAAGTCATCCTAATTTGCTC 59.933 47.826 0.00 0.00 0.00 4.26
802 912 3.313526 CCCAAGTCATCCTAATTTGCTCG 59.686 47.826 0.00 0.00 0.00 5.03
803 913 3.242870 CCAAGTCATCCTAATTTGCTCGC 60.243 47.826 0.00 0.00 0.00 5.03
804 914 2.565841 AGTCATCCTAATTTGCTCGCC 58.434 47.619 0.00 0.00 0.00 5.54
805 915 2.171448 AGTCATCCTAATTTGCTCGCCT 59.829 45.455 0.00 0.00 0.00 5.52
806 916 2.289002 GTCATCCTAATTTGCTCGCCTG 59.711 50.000 0.00 0.00 0.00 4.85
807 917 1.002033 CATCCTAATTTGCTCGCCTGC 60.002 52.381 0.00 0.00 0.00 4.85
808 918 1.089481 TCCTAATTTGCTCGCCTGCG 61.089 55.000 4.92 4.92 41.35 5.18
809 919 1.089481 CCTAATTTGCTCGCCTGCGA 61.089 55.000 14.13 14.13 46.87 5.10
832 942 4.688419 CGCTGCGGCCACAAACTG 62.688 66.667 15.40 0.00 34.44 3.16
833 943 3.286751 GCTGCGGCCACAAACTGA 61.287 61.111 6.12 0.00 0.00 3.41
834 944 2.844451 GCTGCGGCCACAAACTGAA 61.844 57.895 6.12 0.00 0.00 3.02
835 945 1.283793 CTGCGGCCACAAACTGAAG 59.716 57.895 2.24 0.00 0.00 3.02
840 950 1.812324 CGGCCACAAACTGAAGTACCA 60.812 52.381 2.24 0.00 0.00 3.25
900 1019 3.128589 AGCGGCGTTGAAACATGAAATAT 59.871 39.130 9.37 0.00 0.00 1.28
905 1052 6.042143 GGCGTTGAAACATGAAATATCCATT 58.958 36.000 0.00 0.00 0.00 3.16
965 1144 6.157123 TCCTAGATAGATCTGCGATCTCCTTA 59.843 42.308 19.61 11.80 39.34 2.69
966 1145 6.826231 CCTAGATAGATCTGCGATCTCCTTAA 59.174 42.308 19.61 7.17 39.34 1.85
967 1146 7.502226 CCTAGATAGATCTGCGATCTCCTTAAT 59.498 40.741 19.61 10.67 39.34 1.40
968 1147 7.716799 AGATAGATCTGCGATCTCCTTAATT 57.283 36.000 19.61 2.58 34.34 1.40
987 1176 1.737838 TTGCTCCAATCATGTCGTCC 58.262 50.000 0.00 0.00 0.00 4.79
1095 1284 4.082523 ATCACCGGCTCCCACGTG 62.083 66.667 9.08 9.08 0.00 4.49
1144 1333 3.424780 AAAACGGTCCCCAACGGCT 62.425 57.895 0.00 0.00 0.00 5.52
1264 1453 1.899437 CTTCCTTACCAGCCTCGGCA 61.899 60.000 11.02 0.00 44.88 5.69
1339 1531 4.790962 ATGGAGCCGTGCAGCAGG 62.791 66.667 8.20 8.20 34.23 4.85
1373 1571 1.926426 AATGGCTACTGGGGCTGGAC 61.926 60.000 0.00 0.00 0.00 4.02
1404 1602 2.030274 CGACAAGGAAAATCCCAACCAC 60.030 50.000 0.00 0.00 37.19 4.16
1406 1604 2.698274 ACAAGGAAAATCCCAACCACAC 59.302 45.455 0.00 0.00 37.19 3.82
1559 1769 4.760047 GCACCCAGCCGACGTGAT 62.760 66.667 0.00 0.00 37.23 3.06
1632 1842 1.072505 GTCCCCCGTCTTCAAAGCA 59.927 57.895 0.00 0.00 0.00 3.91
1644 1854 0.541998 TCAAAGCAGACCTCGAGGGA 60.542 55.000 34.04 16.65 40.27 4.20
1765 1981 1.235281 GGCGGACAACCAACTTCCTC 61.235 60.000 0.00 0.00 35.59 3.71
1777 1993 3.125829 CCAACTTCCTCACATGATGAACG 59.874 47.826 0.00 0.00 36.69 3.95
1784 2000 2.076100 TCACATGATGAACGAGCAACC 58.924 47.619 0.00 0.00 33.02 3.77
1998 2217 3.173668 TGTCCCGGTAATCTGAAATCG 57.826 47.619 0.00 0.00 0.00 3.34
2004 2223 5.069383 TCCCGGTAATCTGAAATCGTTCATA 59.931 40.000 0.00 0.00 42.85 2.15
2028 2247 0.661552 CCGATGGATTTGAGCAGCTG 59.338 55.000 10.11 10.11 0.00 4.24
2094 2337 0.036732 TGCCGTGATTCTTCTGCCTT 59.963 50.000 0.00 0.00 0.00 4.35
2145 2418 4.787598 AGCAACAGAATTTTCATGTCGAC 58.212 39.130 9.11 9.11 0.00 4.20
2151 2424 9.345517 CAACAGAATTTTCATGTCGACATATTT 57.654 29.630 29.52 16.57 34.26 1.40
2179 2461 1.684983 TCGGGTTTATTAGCTCCTCGG 59.315 52.381 0.00 0.00 0.00 4.63
2180 2462 1.411612 CGGGTTTATTAGCTCCTCGGT 59.588 52.381 0.00 0.00 0.00 4.69
2181 2463 2.802057 CGGGTTTATTAGCTCCTCGGTG 60.802 54.545 0.00 0.00 0.00 4.94
2187 2469 5.927281 TTATTAGCTCCTCGGTGTTTAGT 57.073 39.130 0.00 0.00 0.00 2.24
2299 2877 1.108727 TACCCAACTCGACCACACGT 61.109 55.000 0.00 0.00 34.70 4.49
2308 2886 1.805945 GACCACACGTCTGGATCGC 60.806 63.158 17.45 0.00 38.57 4.58
2341 3077 0.234625 TTGCACGAATCTTGACACGC 59.765 50.000 0.00 0.00 0.00 5.34
2344 3080 1.135972 GCACGAATCTTGACACGCAAT 60.136 47.619 0.00 0.00 35.59 3.56
2354 3090 2.784347 TGACACGCAATGGTGGATTTA 58.216 42.857 6.77 0.00 42.23 1.40
2465 3454 0.598065 GAACTGCTTTTCGCCCACAT 59.402 50.000 0.00 0.00 38.05 3.21
2502 3491 3.276091 CGCGTGTGGGCAAACTGA 61.276 61.111 0.00 0.00 0.00 3.41
2527 3516 1.884579 CACCCACACGACACTACTACT 59.115 52.381 0.00 0.00 0.00 2.57
2568 3558 2.713154 GCGAACGTGGCAACTTGT 59.287 55.556 6.96 0.00 37.61 3.16
2621 3621 0.888736 ATGGCAACTGCAGTTACGCA 60.889 50.000 31.28 24.54 44.36 5.24
2692 3692 3.966215 AACTGCAGTTGCGCGTAT 58.034 50.000 30.66 4.24 45.83 3.06
2862 4106 1.635844 TGATTACACGCGGCAACTAG 58.364 50.000 12.47 0.00 0.00 2.57
2929 4174 5.243730 AGTTGCCATGCTTTTACAACTACAT 59.756 36.000 4.97 0.00 46.66 2.29
2938 4217 5.286082 GCTTTTACAACTACATTTGCCATCG 59.714 40.000 0.00 0.00 0.00 3.84
2953 4232 2.607187 CCATCGCGGATAACTACATCC 58.393 52.381 6.13 0.00 41.06 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.656693 AGACAAATTCAGGGTCTGTAAATCAG 59.343 38.462 0.00 0.00 40.21 2.90
6 7 7.654022 AAAAGACAAATTCAGGGTCTGTAAA 57.346 32.000 0.00 0.00 40.80 2.01
7 8 7.488322 CAAAAAGACAAATTCAGGGTCTGTAA 58.512 34.615 0.00 0.00 40.80 2.41
8 9 6.460953 GCAAAAAGACAAATTCAGGGTCTGTA 60.461 38.462 0.00 0.00 40.80 2.74
9 10 5.682212 GCAAAAAGACAAATTCAGGGTCTGT 60.682 40.000 0.00 0.00 40.80 3.41
10 11 4.746611 GCAAAAAGACAAATTCAGGGTCTG 59.253 41.667 0.00 0.00 40.80 3.51
11 12 4.202253 GGCAAAAAGACAAATTCAGGGTCT 60.202 41.667 0.00 0.00 43.35 3.85
12 13 4.058124 GGCAAAAAGACAAATTCAGGGTC 58.942 43.478 0.00 0.00 0.00 4.46
13 14 3.454082 TGGCAAAAAGACAAATTCAGGGT 59.546 39.130 0.00 0.00 26.55 4.34
14 15 4.070630 TGGCAAAAAGACAAATTCAGGG 57.929 40.909 0.00 0.00 26.55 4.45
15 16 5.358922 TCTTGGCAAAAAGACAAATTCAGG 58.641 37.500 0.00 0.00 46.79 3.86
16 17 6.044682 ACTCTTGGCAAAAAGACAAATTCAG 58.955 36.000 14.28 0.00 46.79 3.02
17 18 5.976458 ACTCTTGGCAAAAAGACAAATTCA 58.024 33.333 14.28 0.00 46.79 2.57
18 19 6.908870 AACTCTTGGCAAAAAGACAAATTC 57.091 33.333 14.28 0.00 46.79 2.17
19 20 7.105588 AGAAACTCTTGGCAAAAAGACAAATT 58.894 30.769 14.28 3.80 46.79 1.82
20 21 6.643388 AGAAACTCTTGGCAAAAAGACAAAT 58.357 32.000 14.28 0.00 46.79 2.32
21 22 6.036577 AGAAACTCTTGGCAAAAAGACAAA 57.963 33.333 14.28 0.00 46.79 2.83
22 23 5.184864 TGAGAAACTCTTGGCAAAAAGACAA 59.815 36.000 14.28 0.00 44.95 3.18
23 24 4.704540 TGAGAAACTCTTGGCAAAAAGACA 59.295 37.500 14.28 0.61 32.75 3.41
24 25 5.163612 ACTGAGAAACTCTTGGCAAAAAGAC 60.164 40.000 14.28 6.90 32.75 3.01
25 26 4.949856 ACTGAGAAACTCTTGGCAAAAAGA 59.050 37.500 14.28 2.14 34.97 2.52
26 27 5.254339 ACTGAGAAACTCTTGGCAAAAAG 57.746 39.130 0.00 4.56 0.00 2.27
27 28 5.047377 ACAACTGAGAAACTCTTGGCAAAAA 60.047 36.000 0.00 0.00 0.00 1.94
28 29 4.462483 ACAACTGAGAAACTCTTGGCAAAA 59.538 37.500 0.00 0.00 0.00 2.44
29 30 4.016444 ACAACTGAGAAACTCTTGGCAAA 58.984 39.130 0.00 0.00 0.00 3.68
30 31 3.620488 ACAACTGAGAAACTCTTGGCAA 58.380 40.909 0.00 0.00 0.00 4.52
31 32 3.206150 GACAACTGAGAAACTCTTGGCA 58.794 45.455 0.00 0.00 28.21 4.92
32 33 2.550180 GGACAACTGAGAAACTCTTGGC 59.450 50.000 0.00 0.00 0.00 4.52
33 34 3.808728 TGGACAACTGAGAAACTCTTGG 58.191 45.455 0.00 0.00 0.00 3.61
34 35 5.818136 TTTGGACAACTGAGAAACTCTTG 57.182 39.130 0.00 0.00 0.00 3.02
35 36 6.122277 TCATTTGGACAACTGAGAAACTCTT 58.878 36.000 1.54 0.00 0.00 2.85
36 37 5.684704 TCATTTGGACAACTGAGAAACTCT 58.315 37.500 1.54 0.00 0.00 3.24
37 38 6.566197 ATCATTTGGACAACTGAGAAACTC 57.434 37.500 10.22 0.00 34.26 3.01
38 39 6.966534 AATCATTTGGACAACTGAGAAACT 57.033 33.333 10.22 0.00 34.26 2.66
39 40 7.202526 TCAAATCATTTGGACAACTGAGAAAC 58.797 34.615 10.30 0.00 40.98 2.78
40 41 7.345422 TCAAATCATTTGGACAACTGAGAAA 57.655 32.000 10.30 0.00 40.98 2.52
41 42 6.957920 TCAAATCATTTGGACAACTGAGAA 57.042 33.333 10.30 0.00 40.98 2.87
42 43 6.957920 TTCAAATCATTTGGACAACTGAGA 57.042 33.333 10.30 1.55 40.98 3.27
43 44 8.597662 ATTTTCAAATCATTTGGACAACTGAG 57.402 30.769 10.30 0.00 40.98 3.35
44 45 8.961294 AATTTTCAAATCATTTGGACAACTGA 57.039 26.923 10.30 7.42 40.98 3.41
46 47 9.492973 CCTAATTTTCAAATCATTTGGACAACT 57.507 29.630 10.30 0.00 40.98 3.16
47 48 8.720562 CCCTAATTTTCAAATCATTTGGACAAC 58.279 33.333 10.30 0.00 40.98 3.32
48 49 7.390162 GCCCTAATTTTCAAATCATTTGGACAA 59.610 33.333 10.30 1.78 40.98 3.18
49 50 6.878389 GCCCTAATTTTCAAATCATTTGGACA 59.122 34.615 10.30 0.00 40.98 4.02
50 51 6.035975 CGCCCTAATTTTCAAATCATTTGGAC 59.964 38.462 10.30 0.00 40.98 4.02
51 52 6.105333 CGCCCTAATTTTCAAATCATTTGGA 58.895 36.000 10.30 0.00 40.98 3.53
52 53 5.294060 CCGCCCTAATTTTCAAATCATTTGG 59.706 40.000 10.30 0.00 40.98 3.28
53 54 6.035975 GTCCGCCCTAATTTTCAAATCATTTG 59.964 38.462 3.46 3.46 41.96 2.32
54 55 6.106003 GTCCGCCCTAATTTTCAAATCATTT 58.894 36.000 0.00 0.00 0.00 2.32
55 56 5.395214 GGTCCGCCCTAATTTTCAAATCATT 60.395 40.000 0.00 0.00 0.00 2.57
56 57 4.099419 GGTCCGCCCTAATTTTCAAATCAT 59.901 41.667 0.00 0.00 0.00 2.45
57 58 3.445805 GGTCCGCCCTAATTTTCAAATCA 59.554 43.478 0.00 0.00 0.00 2.57
58 59 3.699538 AGGTCCGCCCTAATTTTCAAATC 59.300 43.478 0.00 0.00 43.87 2.17
59 60 3.699538 GAGGTCCGCCCTAATTTTCAAAT 59.300 43.478 0.00 0.00 46.51 2.32
60 61 3.086282 GAGGTCCGCCCTAATTTTCAAA 58.914 45.455 0.00 0.00 46.51 2.69
61 62 2.718563 GAGGTCCGCCCTAATTTTCAA 58.281 47.619 0.00 0.00 46.51 2.69
62 63 1.406341 CGAGGTCCGCCCTAATTTTCA 60.406 52.381 0.00 0.00 46.51 2.69
63 64 1.296727 CGAGGTCCGCCCTAATTTTC 58.703 55.000 0.00 0.00 46.51 2.29
64 65 3.471354 CGAGGTCCGCCCTAATTTT 57.529 52.632 0.00 0.00 46.51 1.82
74 75 1.705337 AATTTGATGCGCGAGGTCCG 61.705 55.000 12.10 0.00 42.21 4.79
75 76 0.248215 CAATTTGATGCGCGAGGTCC 60.248 55.000 12.10 0.00 0.00 4.46
76 77 0.447801 ACAATTTGATGCGCGAGGTC 59.552 50.000 12.10 4.36 0.00 3.85
77 78 0.447801 GACAATTTGATGCGCGAGGT 59.552 50.000 12.10 0.00 0.00 3.85
78 79 0.729116 AGACAATTTGATGCGCGAGG 59.271 50.000 12.10 0.00 0.00 4.63
79 80 2.285834 GGTAGACAATTTGATGCGCGAG 60.286 50.000 12.10 0.00 0.00 5.03
80 81 1.663643 GGTAGACAATTTGATGCGCGA 59.336 47.619 12.10 0.00 0.00 5.87
81 82 1.592110 CGGTAGACAATTTGATGCGCG 60.592 52.381 0.00 0.00 0.00 6.86
82 83 1.396996 ACGGTAGACAATTTGATGCGC 59.603 47.619 0.00 0.00 0.00 6.09
83 84 2.223021 CCACGGTAGACAATTTGATGCG 60.223 50.000 2.79 0.00 0.00 4.73
84 85 2.097466 CCCACGGTAGACAATTTGATGC 59.903 50.000 2.79 0.00 0.00 3.91
85 86 3.605634 TCCCACGGTAGACAATTTGATG 58.394 45.455 2.79 0.00 0.00 3.07
86 87 3.992943 TCCCACGGTAGACAATTTGAT 57.007 42.857 2.79 0.00 0.00 2.57
87 88 3.773418 TTCCCACGGTAGACAATTTGA 57.227 42.857 2.79 0.00 0.00 2.69
88 89 4.839668 TTTTCCCACGGTAGACAATTTG 57.160 40.909 0.00 0.00 0.00 2.32
151 152 8.450964 GCTTATCTGCATCTGTGTTAAGTAAAA 58.549 33.333 0.00 0.00 0.00 1.52
152 153 7.065803 GGCTTATCTGCATCTGTGTTAAGTAAA 59.934 37.037 0.00 0.00 34.04 2.01
153 154 6.538742 GGCTTATCTGCATCTGTGTTAAGTAA 59.461 38.462 0.00 0.00 34.04 2.24
154 155 6.049149 GGCTTATCTGCATCTGTGTTAAGTA 58.951 40.000 0.00 0.00 34.04 2.24
155 156 4.878397 GGCTTATCTGCATCTGTGTTAAGT 59.122 41.667 0.00 0.00 34.04 2.24
156 157 4.274459 GGGCTTATCTGCATCTGTGTTAAG 59.726 45.833 0.00 0.00 34.04 1.85
157 158 4.199310 GGGCTTATCTGCATCTGTGTTAA 58.801 43.478 0.00 0.00 34.04 2.01
158 159 3.741075 CGGGCTTATCTGCATCTGTGTTA 60.741 47.826 0.00 0.00 34.04 2.41
159 160 2.648059 GGGCTTATCTGCATCTGTGTT 58.352 47.619 0.00 0.00 34.04 3.32
160 161 1.473965 CGGGCTTATCTGCATCTGTGT 60.474 52.381 0.00 0.00 34.04 3.72
161 162 1.224075 CGGGCTTATCTGCATCTGTG 58.776 55.000 0.00 0.00 34.04 3.66
162 163 0.107456 CCGGGCTTATCTGCATCTGT 59.893 55.000 0.00 0.00 34.04 3.41
163 164 0.394192 TCCGGGCTTATCTGCATCTG 59.606 55.000 0.00 0.00 34.04 2.90
164 165 0.394565 GTCCGGGCTTATCTGCATCT 59.605 55.000 0.00 0.00 34.04 2.90
165 166 0.394565 AGTCCGGGCTTATCTGCATC 59.605 55.000 0.35 0.00 34.04 3.91
166 167 0.394565 GAGTCCGGGCTTATCTGCAT 59.605 55.000 11.49 0.00 34.04 3.96
167 168 0.975556 TGAGTCCGGGCTTATCTGCA 60.976 55.000 11.49 0.00 34.04 4.41
168 169 0.249657 CTGAGTCCGGGCTTATCTGC 60.250 60.000 11.49 0.00 0.00 4.26
169 170 1.403814 TCTGAGTCCGGGCTTATCTG 58.596 55.000 11.49 1.64 0.00 2.90
170 171 2.160721 TTCTGAGTCCGGGCTTATCT 57.839 50.000 11.49 0.00 0.00 1.98
171 172 2.981859 TTTCTGAGTCCGGGCTTATC 57.018 50.000 11.49 0.00 0.00 1.75
172 173 2.092914 CCTTTTCTGAGTCCGGGCTTAT 60.093 50.000 11.49 0.00 0.00 1.73
173 174 1.278127 CCTTTTCTGAGTCCGGGCTTA 59.722 52.381 11.49 4.71 0.00 3.09
174 175 0.036875 CCTTTTCTGAGTCCGGGCTT 59.963 55.000 11.49 0.00 0.00 4.35
175 176 0.836400 TCCTTTTCTGAGTCCGGGCT 60.836 55.000 9.26 9.26 0.00 5.19
176 177 0.253327 ATCCTTTTCTGAGTCCGGGC 59.747 55.000 0.00 0.00 0.00 6.13
177 178 2.789409 AATCCTTTTCTGAGTCCGGG 57.211 50.000 0.00 0.00 0.00 5.73
190 191 9.674068 GAAGAGGTAAAACTATGAGAAATCCTT 57.326 33.333 0.00 0.00 0.00 3.36
191 192 9.052365 AGAAGAGGTAAAACTATGAGAAATCCT 57.948 33.333 0.00 0.00 0.00 3.24
192 193 9.320352 GAGAAGAGGTAAAACTATGAGAAATCC 57.680 37.037 0.00 0.00 0.00 3.01
193 194 9.026074 CGAGAAGAGGTAAAACTATGAGAAATC 57.974 37.037 0.00 0.00 0.00 2.17
194 195 7.982354 CCGAGAAGAGGTAAAACTATGAGAAAT 59.018 37.037 0.00 0.00 0.00 2.17
195 196 7.321153 CCGAGAAGAGGTAAAACTATGAGAAA 58.679 38.462 0.00 0.00 0.00 2.52
196 197 6.627508 GCCGAGAAGAGGTAAAACTATGAGAA 60.628 42.308 0.00 0.00 0.00 2.87
197 198 5.163540 GCCGAGAAGAGGTAAAACTATGAGA 60.164 44.000 0.00 0.00 0.00 3.27
198 199 5.044558 GCCGAGAAGAGGTAAAACTATGAG 58.955 45.833 0.00 0.00 0.00 2.90
199 200 4.142004 GGCCGAGAAGAGGTAAAACTATGA 60.142 45.833 0.00 0.00 0.00 2.15
200 201 4.120589 GGCCGAGAAGAGGTAAAACTATG 58.879 47.826 0.00 0.00 0.00 2.23
201 202 4.031611 AGGCCGAGAAGAGGTAAAACTAT 58.968 43.478 0.00 0.00 0.00 2.12
218 219 2.868583 CAGTTTCACTCATATCAGGCCG 59.131 50.000 0.00 0.00 0.00 6.13
221 222 4.701765 CCTCCAGTTTCACTCATATCAGG 58.298 47.826 0.00 0.00 0.00 3.86
237 238 2.103143 CACTCGTAGCGCCTCCAG 59.897 66.667 2.29 0.00 0.00 3.86
242 243 2.881352 GCACTCACTCGTAGCGCC 60.881 66.667 2.29 0.00 0.00 6.53
246 247 4.368756 GAGCGCACTCACTCGTAG 57.631 61.111 11.47 0.00 42.93 3.51
308 309 3.475774 CGTTCGTACCAGGTGCGC 61.476 66.667 24.15 11.00 41.09 6.09
328 329 4.021104 AGGAGATATGCAAGCGCTTGTATA 60.021 41.667 42.60 42.60 46.62 1.47
333 334 2.158842 AGAAGGAGATATGCAAGCGCTT 60.159 45.455 18.98 18.98 39.64 4.68
353 354 1.267806 CAACACAAGCAAGCCCTACAG 59.732 52.381 0.00 0.00 0.00 2.74
375 376 0.921896 ACACATATTCTGCTGGGGCT 59.078 50.000 0.00 0.00 39.59 5.19
385 386 4.023536 ACCAACAAACCGACACACATATTC 60.024 41.667 0.00 0.00 0.00 1.75
387 388 3.482436 ACCAACAAACCGACACACATAT 58.518 40.909 0.00 0.00 0.00 1.78
410 411 2.021457 ACCAACCAGTCCGACAAAAAG 58.979 47.619 0.40 0.00 0.00 2.27
412 413 1.746220 CAACCAACCAGTCCGACAAAA 59.254 47.619 0.40 0.00 0.00 2.44
413 414 1.384525 CAACCAACCAGTCCGACAAA 58.615 50.000 0.40 0.00 0.00 2.83
418 419 1.600023 TAAAGCAACCAACCAGTCCG 58.400 50.000 0.00 0.00 0.00 4.79
448 449 2.376109 TCTCGAAATAGACTTCGCCCT 58.624 47.619 0.99 0.00 46.12 5.19
456 458 6.289901 CGTTTCACTGTTTCTCGAAATAGAC 58.710 40.000 18.84 8.56 40.54 2.59
460 462 3.311322 TGCGTTTCACTGTTTCTCGAAAT 59.689 39.130 0.00 0.00 32.36 2.17
471 473 6.932901 ATGATAATTTTGTGCGTTTCACTG 57.067 33.333 0.00 0.00 45.81 3.66
472 474 7.867403 AGAAATGATAATTTTGTGCGTTTCACT 59.133 29.630 0.00 0.00 45.81 3.41
476 479 7.378181 AGGAGAAATGATAATTTTGTGCGTTT 58.622 30.769 0.00 0.00 0.00 3.60
480 483 6.473455 CGGAAGGAGAAATGATAATTTTGTGC 59.527 38.462 0.00 0.00 0.00 4.57
504 507 1.068472 AGCGTCTTGACAGAACCTACG 60.068 52.381 1.59 0.00 0.00 3.51
505 508 2.726832 AGCGTCTTGACAGAACCTAC 57.273 50.000 1.59 0.00 0.00 3.18
514 517 9.245962 ACAATAGTTATATGTAAGCGTCTTGAC 57.754 33.333 2.86 0.00 0.00 3.18
515 518 9.244799 CACAATAGTTATATGTAAGCGTCTTGA 57.755 33.333 2.86 0.00 0.00 3.02
516 519 9.244799 TCACAATAGTTATATGTAAGCGTCTTG 57.755 33.333 2.86 0.00 0.00 3.02
619 627 3.692791 TCTCAGATACACGGATGAACG 57.307 47.619 0.00 0.00 40.31 3.95
626 634 3.921021 GCCGATATTTCTCAGATACACGG 59.079 47.826 0.00 0.00 36.38 4.94
627 635 3.921021 GGCCGATATTTCTCAGATACACG 59.079 47.826 0.00 0.00 0.00 4.49
628 636 3.921021 CGGCCGATATTTCTCAGATACAC 59.079 47.826 24.07 0.00 0.00 2.90
631 639 2.826128 AGCGGCCGATATTTCTCAGATA 59.174 45.455 33.48 0.00 0.00 1.98
638 646 1.774639 TACGAAGCGGCCGATATTTC 58.225 50.000 33.48 22.95 0.00 2.17
757 866 7.148086 TGGGCTACAATTAATTAGCAGAAGTTG 60.148 37.037 19.65 7.23 42.22 3.16
758 867 6.889722 TGGGCTACAATTAATTAGCAGAAGTT 59.110 34.615 19.65 0.00 42.22 2.66
760 869 6.942532 TGGGCTACAATTAATTAGCAGAAG 57.057 37.500 19.65 2.53 42.22 2.85
815 925 4.688419 CAGTTTGTGGCCGCAGCG 62.688 66.667 20.15 8.18 41.24 5.18
816 926 2.737932 CTTCAGTTTGTGGCCGCAGC 62.738 60.000 20.15 16.10 38.76 5.25
817 927 1.283793 CTTCAGTTTGTGGCCGCAG 59.716 57.895 20.15 8.08 0.00 5.18
818 928 0.179043 TACTTCAGTTTGTGGCCGCA 60.179 50.000 16.89 16.89 0.00 5.69
819 929 0.237498 GTACTTCAGTTTGTGGCCGC 59.763 55.000 10.11 10.11 0.00 6.53
820 930 0.872388 GGTACTTCAGTTTGTGGCCG 59.128 55.000 0.00 0.00 0.00 6.13
821 931 1.975660 TGGTACTTCAGTTTGTGGCC 58.024 50.000 0.00 0.00 0.00 5.36
822 932 3.630312 TCTTTGGTACTTCAGTTTGTGGC 59.370 43.478 0.00 0.00 0.00 5.01
823 933 7.504924 TTATCTTTGGTACTTCAGTTTGTGG 57.495 36.000 0.00 0.00 0.00 4.17
832 942 9.952188 GGAGCAAATTATTATCTTTGGTACTTC 57.048 33.333 7.10 0.00 41.62 3.01
833 943 8.914011 GGGAGCAAATTATTATCTTTGGTACTT 58.086 33.333 11.64 0.00 41.34 2.24
834 944 7.228706 CGGGAGCAAATTATTATCTTTGGTACT 59.771 37.037 11.64 0.00 41.34 2.73
835 945 7.012989 ACGGGAGCAAATTATTATCTTTGGTAC 59.987 37.037 6.22 6.22 41.62 3.34
840 950 9.220767 GAGATACGGGAGCAAATTATTATCTTT 57.779 33.333 0.00 0.00 0.00 2.52
851 961 3.019799 AGAGAGAGATACGGGAGCAAA 57.980 47.619 0.00 0.00 0.00 3.68
852 962 2.738587 AGAGAGAGATACGGGAGCAA 57.261 50.000 0.00 0.00 0.00 3.91
855 965 4.224147 TGGAGATAGAGAGAGATACGGGAG 59.776 50.000 0.00 0.00 0.00 4.30
929 1076 3.511477 TCTATCTAGGATTCCAGGTGCC 58.489 50.000 5.29 0.00 0.00 5.01
930 1077 5.022787 AGATCTATCTAGGATTCCAGGTGC 58.977 45.833 5.29 0.00 34.85 5.01
933 1080 4.097741 CGCAGATCTATCTAGGATTCCAGG 59.902 50.000 5.29 0.00 34.85 4.45
934 1081 4.946772 TCGCAGATCTATCTAGGATTCCAG 59.053 45.833 5.29 0.89 34.85 3.86
936 1083 5.827797 AGATCGCAGATCTATCTAGGATTCC 59.172 44.000 16.15 0.00 45.12 3.01
937 1084 6.017109 GGAGATCGCAGATCTATCTAGGATTC 60.017 46.154 17.22 5.36 45.12 2.52
939 1086 5.132648 AGGAGATCGCAGATCTATCTAGGAT 59.867 44.000 17.22 5.20 45.12 3.24
940 1087 4.473196 AGGAGATCGCAGATCTATCTAGGA 59.527 45.833 17.22 0.00 45.12 2.94
965 1144 3.129287 GGACGACATGATTGGAGCAAATT 59.871 43.478 0.00 0.00 0.00 1.82
966 1145 2.684881 GGACGACATGATTGGAGCAAAT 59.315 45.455 0.00 0.00 0.00 2.32
967 1146 2.083774 GGACGACATGATTGGAGCAAA 58.916 47.619 0.00 0.00 0.00 3.68
968 1147 1.278985 AGGACGACATGATTGGAGCAA 59.721 47.619 0.00 0.00 0.00 3.91
987 1176 0.933097 CCGACATTGGCTTGATCGAG 59.067 55.000 5.50 5.50 34.77 4.04
1264 1453 2.665185 GAACTCTGCCGTGGCGTT 60.665 61.111 6.37 4.40 45.51 4.84
1339 1531 1.488527 CCATTAGCCGAGTAGCGTTC 58.511 55.000 0.00 0.00 38.67 3.95
1632 1842 2.647158 GGCGTTTCCCTCGAGGTCT 61.647 63.158 29.25 0.00 36.75 3.85
1765 1981 1.131126 GGGTTGCTCGTTCATCATGTG 59.869 52.381 0.00 0.00 0.00 3.21
1777 1993 2.514824 GGCCTGATCGGGTTGCTC 60.515 66.667 21.88 4.55 0.00 4.26
1948 2167 2.401766 CCATGCACGCCTCCTTGAC 61.402 63.158 0.00 0.00 0.00 3.18
1998 2217 2.550830 ATCCATCGGTGGCTATGAAC 57.449 50.000 10.80 0.00 45.63 3.18
2004 2223 0.749454 GCTCAAATCCATCGGTGGCT 60.749 55.000 10.80 0.00 45.63 4.75
2151 2424 6.042781 AGGAGCTAATAAACCCGAACATATGA 59.957 38.462 10.38 0.00 0.00 2.15
2163 2436 6.104665 ACTAAACACCGAGGAGCTAATAAAC 58.895 40.000 0.00 0.00 0.00 2.01
2164 2437 6.290294 ACTAAACACCGAGGAGCTAATAAA 57.710 37.500 0.00 0.00 0.00 1.40
2238 2520 7.096763 GGTGTTAGTGTTTTCGATAACTTTTGC 60.097 37.037 17.72 7.81 0.00 3.68
2291 2869 2.261671 GCGATCCAGACGTGTGGT 59.738 61.111 28.90 17.45 38.88 4.16
2299 2877 1.215382 CAGTGAACGGCGATCCAGA 59.785 57.895 16.62 0.00 0.00 3.86
2308 2886 1.594518 CGTGCAAAAGACAGTGAACGG 60.595 52.381 0.00 0.00 42.08 4.44
2341 3077 2.824936 TGGCACACTAAATCCACCATTG 59.175 45.455 0.00 0.00 0.00 2.82
2496 3485 3.066203 GTCGTGTGGGTGAAAATCAGTTT 59.934 43.478 0.00 0.00 0.00 2.66
2502 3491 2.341846 AGTGTCGTGTGGGTGAAAAT 57.658 45.000 0.00 0.00 0.00 1.82
2527 3516 1.693062 ACTGCAATTGCCATCCACAAA 59.307 42.857 26.94 4.58 41.18 2.83
2568 3558 4.518249 TCACAGTTTCCATGTGTGTGTAA 58.482 39.130 11.76 0.00 46.49 2.41
2621 3621 0.179078 TGTACCGAGTTGCCACGTTT 60.179 50.000 0.00 0.00 0.00 3.60
2692 3692 2.621055 GTGTGTTTATCTGGTTGCCACA 59.379 45.455 0.00 0.00 0.00 4.17
2862 4106 9.003658 ACTATAGTTGCCATGTCTAATTTATGC 57.996 33.333 0.00 0.00 0.00 3.14
2929 4174 2.206750 GTAGTTATCCGCGATGGCAAA 58.793 47.619 8.23 0.00 39.92 3.68
3039 4319 3.207547 CTCCACCTCGTGCGTGTGA 62.208 63.158 14.68 4.83 31.34 3.58
3050 4330 4.936802 ACAAGTACTACTCATCTCCACCT 58.063 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.