Multiple sequence alignment - TraesCS5D01G164000

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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 TraesCS5D01G164000 chr5D 100.000 5535 0 0 1 5535 255580190 255574656 0.000000e+00 10222.0
1 TraesCS5D01G164000 chr5D 93.085 188 8 4 2476 2661 255577495 255577311 2.540000e-68 270.0
2 TraesCS5D01G164000 chr5D 93.085 188 8 4 2696 2880 255577715 255577530 2.540000e-68 270.0
3 TraesCS5D01G164000 chr5D 83.268 257 35 4 5287 5535 133538809 133539065 4.310000e-56 230.0
4 TraesCS5D01G164000 chr5D 87.209 86 7 2 5069 5151 133538438 133538522 1.640000e-15 95.3
5 TraesCS5D01G164000 chr5D 74.860 179 45 0 1669 1847 16940282 16940104 1.280000e-11 82.4
6 TraesCS5D01G164000 chr5B 96.285 3311 94 12 1538 4825 289163756 289160452 0.000000e+00 5406.0
7 TraesCS5D01G164000 chr5B 95.926 810 20 7 715 1512 289164892 289164084 0.000000e+00 1301.0
8 TraesCS5D01G164000 chr5B 92.799 736 45 4 1 733 289165636 289164906 0.000000e+00 1059.0
9 TraesCS5D01G164000 chr5B 93.048 187 11 2 2476 2661 289162596 289162411 7.070000e-69 272.0
10 TraesCS5D01G164000 chr5B 92.473 186 13 1 2696 2880 289162816 289162631 1.180000e-66 265.0
11 TraesCS5D01G164000 chr5A 96.478 2186 55 9 2696 4865 338895246 338893067 0.000000e+00 3591.0
12 TraesCS5D01G164000 chr5A 95.358 1939 60 15 746 2661 338896993 338895062 0.000000e+00 3055.0
13 TraesCS5D01G164000 chr5A 91.615 322 23 2 4911 5231 338893061 338892743 5.090000e-120 442.0
14 TraesCS5D01G164000 chr5A 86.260 262 21 5 5289 5535 338888545 338888284 2.540000e-68 270.0
15 TraesCS5D01G164000 chr5A 79.882 169 22 7 5075 5231 52405609 52405777 4.530000e-21 113.0
16 TraesCS5D01G164000 chr4D 86.166 253 26 6 5291 5535 128909545 128909294 1.180000e-66 265.0
17 TraesCS5D01G164000 chr4D 87.111 225 28 1 5312 5535 343092742 343092518 2.560000e-63 254.0
18 TraesCS5D01G164000 chr4D 81.364 220 40 1 2475 2694 25165126 25164908 1.580000e-40 178.0
19 TraesCS5D01G164000 chr4D 83.871 186 30 0 2696 2881 25165125 25164940 1.580000e-40 178.0
20 TraesCS5D01G164000 chr4D 80.658 243 36 8 2696 2927 95126204 95125962 1.580000e-40 178.0
21 TraesCS5D01G164000 chr4D 88.028 142 17 0 5087 5228 128909826 128909685 9.540000e-38 169.0
22 TraesCS5D01G164000 chr3D 87.727 220 26 1 2475 2694 313180634 313180416 7.120000e-64 255.0
23 TraesCS5D01G164000 chr3D 89.730 185 19 0 2696 2880 313180633 313180449 2.580000e-58 237.0
24 TraesCS5D01G164000 chr3D 86.885 183 24 0 2696 2878 67243918 67243736 7.270000e-49 206.0
25 TraesCS5D01G164000 chr3D 91.892 37 3 0 2 38 107430686 107430722 1.000000e-02 52.8
26 TraesCS5D01G164000 chr2A 84.127 252 34 2 5290 5535 21147198 21147449 7.170000e-59 239.0
27 TraesCS5D01G164000 chr2A 84.314 204 29 3 5314 5516 413181994 413181793 4.370000e-46 196.0
28 TraesCS5D01G164000 chr2A 87.417 151 15 4 5074 5221 518338240 518338091 2.650000e-38 171.0
29 TraesCS5D01G164000 chr2A 81.553 206 34 4 2488 2692 537553344 537553546 3.430000e-37 167.0
30 TraesCS5D01G164000 chr2A 85.714 147 20 1 5084 5230 595385699 595385844 2.670000e-33 154.0
31 TraesCS5D01G164000 chr1A 83.203 256 35 3 5288 5535 552458659 552458914 1.550000e-55 228.0
32 TraesCS5D01G164000 chr1A 84.000 200 32 0 90 289 497535953 497536152 5.660000e-45 193.0
33 TraesCS5D01G164000 chr3A 84.753 223 33 1 2472 2694 419333875 419334096 7.220000e-54 222.0
34 TraesCS5D01G164000 chr3A 87.363 182 23 0 2696 2877 419333879 419334060 5.620000e-50 209.0
35 TraesCS5D01G164000 chr6D 82.403 233 24 11 5290 5515 147688533 147688755 2.630000e-43 187.0
36 TraesCS5D01G164000 chr6D 86.076 158 19 1 5074 5228 147688236 147688393 3.430000e-37 167.0
37 TraesCS5D01G164000 chr2D 86.826 167 16 3 5069 5232 383561847 383561684 1.220000e-41 182.0
38 TraesCS5D01G164000 chr2D 81.773 203 35 2 2490 2692 400523212 400523412 9.540000e-38 169.0
39 TraesCS5D01G164000 chr2B 85.507 138 20 0 5080 5217 130011678 130011541 1.610000e-30 145.0


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 TraesCS5D01G164000 chr5D 255574656 255580190 5534 True 3587.333333 10222 95.390000 1 5535 3 chr5D.!!$R2 5534
1 TraesCS5D01G164000 chr5B 289160452 289165636 5184 True 1660.600000 5406 94.106200 1 4825 5 chr5B.!!$R1 4824
2 TraesCS5D01G164000 chr5A 338892743 338896993 4250 True 2362.666667 3591 94.483667 746 5231 3 chr5A.!!$R2 4485
3 TraesCS5D01G164000 chr4D 128909294 128909826 532 True 217.000000 265 87.097000 5087 5535 2 chr4D.!!$R4 448

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
441 444 0.539669 CACCTTTCCTTCCCCACCAC 60.540 60.000 0.00 0.0 0.00 4.16 F
532 535 0.672401 GCCGACGAACCAGGATTTCA 60.672 55.000 0.00 0.0 0.00 2.69 F
585 589 0.760945 ACCGCCTAGAGGAAGGATGG 60.761 60.000 14.97 0.0 39.15 3.51 F
847 883 1.376037 CAAAGCGTGTCCCTCCCTC 60.376 63.158 0.00 0.0 0.00 4.30 F
1604 1972 1.815408 GCTCTGCTGTCCTTCCAACAA 60.815 52.381 0.00 0.0 0.00 2.83 F
2679 3049 1.394618 ACACTGGAGCGAGGTAGATC 58.605 55.000 0.00 0.0 0.00 2.75 F
2685 3055 2.158856 TGGAGCGAGGTAGATCGTTAGA 60.159 50.000 0.00 0.0 44.53 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 2028 0.036483 TCCTTGTAGCAGCATCGCAA 60.036 50.000 0.00 0.00 0.00 4.85 R
1901 2269 2.297701 AGTGAAACAAGTGGCACGATT 58.702 42.857 12.71 5.12 41.43 3.34 R
1944 2312 5.224821 AGTTACAAGGTCAGGAGTAAACC 57.775 43.478 0.00 0.00 0.00 3.27 R
2664 3034 2.158856 TCTAACGATCTACCTCGCTCCA 60.159 50.000 0.00 0.00 42.35 3.86 R
3202 3573 3.682696 AGAATCAGCAATCTTGTCAGCA 58.317 40.909 0.00 0.00 0.00 4.41 R
4421 4795 0.106769 TGTGGTCCAAAAGCAGAGCA 60.107 50.000 0.00 0.00 38.12 4.26 R
4546 4921 2.348666 CGGCATAAAACAGGAACGAGAG 59.651 50.000 0.00 0.00 0.00 3.20 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
37 38 8.213679 ACATTTCTAGCATATTACACATGGACT 58.786 33.333 0.00 0.00 0.00 3.85
89 90 9.360093 GCTGAGTTGTGTAGGATCATATATAAC 57.640 37.037 13.33 13.33 0.00 1.89
128 129 5.555017 GGTGATGTGTAGGATCATAGCAAT 58.445 41.667 0.00 0.00 32.53 3.56
156 157 3.448660 TGTCGATGGTGATGATCTTCACT 59.551 43.478 30.03 18.09 44.39 3.41
170 171 5.352293 TGATCTTCACTGTATGTTGTCATGC 59.648 40.000 0.00 0.00 37.23 4.06
172 173 5.062528 TCTTCACTGTATGTTGTCATGCAA 58.937 37.500 0.00 0.00 43.69 4.08
180 181 2.607499 TGTTGTCATGCAAAAGGGGAT 58.393 42.857 0.00 0.00 39.03 3.85
183 184 3.017048 TGTCATGCAAAAGGGGATAGG 57.983 47.619 0.00 0.00 0.00 2.57
198 199 3.325135 GGGATAGGTGGTACAAGGATCAG 59.675 52.174 0.00 0.00 44.16 2.90
237 238 1.585297 AACCCTTGTACAAACGACCG 58.415 50.000 10.03 0.00 0.00 4.79
249 250 3.863424 ACAAACGACCGCTCTAATACATG 59.137 43.478 0.00 0.00 0.00 3.21
274 275 9.112725 TGGACTGTACAATAATGAAGATCATTG 57.887 33.333 14.23 3.82 45.77 2.82
275 276 8.072567 GGACTGTACAATAATGAAGATCATTGC 58.927 37.037 14.23 0.00 45.77 3.56
277 278 8.834465 ACTGTACAATAATGAAGATCATTGCTC 58.166 33.333 14.23 2.44 45.77 4.26
289 291 2.412870 TCATTGCTCAACACAGTACCG 58.587 47.619 0.00 0.00 0.00 4.02
292 294 0.878523 TGCTCAACACAGTACCGCAC 60.879 55.000 0.00 0.00 0.00 5.34
328 330 6.895756 ACCTTCCCCAAATCTAAACCTAAATC 59.104 38.462 0.00 0.00 0.00 2.17
333 335 6.183360 CCCCAAATCTAAACCTAAATCGACAC 60.183 42.308 0.00 0.00 0.00 3.67
341 343 2.809696 ACCTAAATCGACACCCAAAACG 59.190 45.455 0.00 0.00 0.00 3.60
350 352 1.339727 ACACCCAAAACGAGCCCTATC 60.340 52.381 0.00 0.00 0.00 2.08
357 359 0.686769 AACGAGCCCTATCGAACCCT 60.687 55.000 2.78 0.00 45.56 4.34
417 419 3.261897 CCATCGGGCCTTAGATCAGTATT 59.738 47.826 0.84 0.00 0.00 1.89
441 444 0.539669 CACCTTTCCTTCCCCACCAC 60.540 60.000 0.00 0.00 0.00 4.16
450 453 0.695924 TTCCCCACCACGACATCATT 59.304 50.000 0.00 0.00 0.00 2.57
466 469 3.851458 TCATTGAGTCCATCATCCCTG 57.149 47.619 0.00 0.00 37.89 4.45
484 487 1.876156 CTGAGGTCCAAGTGCTTCAAC 59.124 52.381 0.00 0.00 0.00 3.18
509 512 1.758862 CCTCCAAATTGCCATCCTTCC 59.241 52.381 0.00 0.00 0.00 3.46
510 513 2.459644 CTCCAAATTGCCATCCTTCCA 58.540 47.619 0.00 0.00 0.00 3.53
517 520 3.781307 CCATCCTTCCACCGCCGA 61.781 66.667 0.00 0.00 0.00 5.54
531 534 1.693083 CGCCGACGAACCAGGATTTC 61.693 60.000 0.00 0.00 43.93 2.17
532 535 0.672401 GCCGACGAACCAGGATTTCA 60.672 55.000 0.00 0.00 0.00 2.69
533 536 1.076332 CCGACGAACCAGGATTTCAC 58.924 55.000 0.00 0.00 0.00 3.18
534 537 1.337823 CCGACGAACCAGGATTTCACT 60.338 52.381 0.00 0.00 0.00 3.41
536 539 2.157668 CGACGAACCAGGATTTCACTTG 59.842 50.000 0.00 0.00 0.00 3.16
537 540 3.399330 GACGAACCAGGATTTCACTTGA 58.601 45.455 0.00 0.00 0.00 3.02
538 541 3.403038 ACGAACCAGGATTTCACTTGAG 58.597 45.455 0.00 0.00 0.00 3.02
539 542 2.160417 CGAACCAGGATTTCACTTGAGC 59.840 50.000 0.00 0.00 0.00 4.26
585 589 0.760945 ACCGCCTAGAGGAAGGATGG 60.761 60.000 14.97 0.00 39.15 3.51
845 881 2.359975 CCAAAGCGTGTCCCTCCC 60.360 66.667 0.00 0.00 0.00 4.30
846 882 2.750350 CAAAGCGTGTCCCTCCCT 59.250 61.111 0.00 0.00 0.00 4.20
847 883 1.376037 CAAAGCGTGTCCCTCCCTC 60.376 63.158 0.00 0.00 0.00 4.30
848 884 2.593956 AAAGCGTGTCCCTCCCTCC 61.594 63.158 0.00 0.00 0.00 4.30
849 885 3.547787 AAGCGTGTCCCTCCCTCCT 62.548 63.158 0.00 0.00 0.00 3.69
1031 1076 4.090588 TAAGCCACGCCTTCCCCG 62.091 66.667 0.00 0.00 0.00 5.73
1213 1260 3.494573 CCCGCCCTCCTCTATTTACTTTC 60.495 52.174 0.00 0.00 0.00 2.62
1232 1288 6.935167 ACTTTCTGAAGGTCATGTTTTGTTT 58.065 32.000 0.00 0.00 37.19 2.83
1269 1325 6.857964 GGTCATGTTTTGTTTGACAGTATCAG 59.142 38.462 4.85 0.00 41.17 2.90
1588 1956 5.746990 AGACCTACTGTATTGTTTGCTCT 57.253 39.130 0.00 0.00 0.00 4.09
1604 1972 1.815408 GCTCTGCTGTCCTTCCAACAA 60.815 52.381 0.00 0.00 0.00 2.83
1623 1991 3.315191 ACAAGTATTTGCGGGCATGATAC 59.685 43.478 14.70 14.70 37.85 2.24
1901 2269 8.897872 AGACTCGTATCCTTTTTGAAAGTTTA 57.102 30.769 0.00 0.00 0.00 2.01
1944 2312 6.316390 ACTTTTCTGTAGTGTTTCAGACTTGG 59.684 38.462 0.00 0.00 39.87 3.61
2179 2549 6.969366 TGAATTATCGGGCAATGAATTACTG 58.031 36.000 0.00 0.00 0.00 2.74
2519 2889 8.697846 TGCACGTTAATATTAGGCAGTATATC 57.302 34.615 8.30 0.00 0.00 1.63
2669 3039 3.806958 GTTTAACGCTAAACACTGGAGC 58.193 45.455 14.89 0.00 44.29 4.70
2679 3049 1.394618 ACACTGGAGCGAGGTAGATC 58.605 55.000 0.00 0.00 0.00 2.75
2683 3053 2.219458 CTGGAGCGAGGTAGATCGTTA 58.781 52.381 0.00 0.00 44.53 3.18
2685 3055 2.158856 TGGAGCGAGGTAGATCGTTAGA 60.159 50.000 0.00 0.00 44.53 2.10
2734 3104 5.173131 GCAATGCACGTTAATATTAGGCAAC 59.827 40.000 0.00 3.91 33.09 4.17
2752 3122 6.604930 AGGCAACGTATTAATTGTGTTGTAC 58.395 36.000 19.52 15.26 41.38 2.90
3073 3444 3.055891 TGCTGCTACTGCTGTCTAATTCA 60.056 43.478 0.00 0.00 39.81 2.57
3116 3487 4.142534 CCCAGTGATTGCTAACACATTCTG 60.143 45.833 10.79 0.98 39.18 3.02
3169 3540 4.232221 CTCGTAAGGTTAAAAGACAGCGA 58.768 43.478 0.00 0.00 38.47 4.93
3202 3573 2.338577 AGCAACAAGTTGACAGCTCT 57.661 45.000 16.54 0.49 42.93 4.09
3511 3882 7.857885 GCTTCCTGTTTAGTTGCATATATGTTC 59.142 37.037 14.14 5.44 0.00 3.18
3997 4368 6.067263 TGTAAACATGTCCACTTTACTTGC 57.933 37.500 15.06 1.90 33.38 4.01
4142 4513 3.795905 CCATGCTTGGGTTTGCCT 58.204 55.556 10.81 0.00 39.56 4.75
4158 4529 4.339872 TTGCCTTTCAGAATGCATGTTT 57.660 36.364 0.00 0.00 36.50 2.83
4225 4596 7.767659 CCTTGGTATTACTGGTAAAACTACCTC 59.232 40.741 16.24 1.13 40.70 3.85
4232 4603 3.698040 CTGGTAAAACTACCTCGGAGCTA 59.302 47.826 0.00 0.00 40.70 3.32
4233 4604 4.284178 TGGTAAAACTACCTCGGAGCTAT 58.716 43.478 0.00 0.00 40.70 2.97
4234 4605 5.448654 TGGTAAAACTACCTCGGAGCTATA 58.551 41.667 0.00 0.00 40.70 1.31
4270 4641 4.380531 TGCTTTGAGTCATTTCTTCGACT 58.619 39.130 0.00 0.00 45.07 4.18
4387 4760 6.587608 GCATTTGTTTACTTTCCATCTTCCTG 59.412 38.462 0.00 0.00 0.00 3.86
4454 4828 4.661222 TGGACCACATTTATTCTTCAGCA 58.339 39.130 0.00 0.00 0.00 4.41
4544 4919 2.659244 TCCGGTGAAACGCGTGAC 60.659 61.111 14.98 11.01 38.12 3.67
4546 4921 3.708734 CGGTGAAACGCGTGACCC 61.709 66.667 22.69 15.54 38.12 4.46
4615 4990 3.517100 AGCTACAGATGGAGATTGTGTGT 59.483 43.478 0.00 0.00 0.00 3.72
4714 5089 6.402550 GCATTCGAGTTAGCAAAAAGAGATGA 60.403 38.462 0.00 0.00 0.00 2.92
4825 5217 6.402983 GCAATTCTGTCGAATGTGAGAATTCT 60.403 38.462 7.95 7.95 41.20 2.40
4830 5222 7.776107 TCTGTCGAATGTGAGAATTCTATCTT 58.224 34.615 8.25 0.00 34.90 2.40
4840 5232 7.099764 GTGAGAATTCTATCTTGTTCCTGTCA 58.900 38.462 8.25 0.00 0.00 3.58
4859 5251 4.099113 TGTCAATGCAACATTCCTGTCAAA 59.901 37.500 0.00 0.00 33.36 2.69
4862 5254 5.010820 TCAATGCAACATTCCTGTCAAATCA 59.989 36.000 0.00 0.00 33.36 2.57
4865 5257 5.069318 TGCAACATTCCTGTCAAATCAGTA 58.931 37.500 0.00 0.00 33.36 2.74
4866 5258 5.711506 TGCAACATTCCTGTCAAATCAGTAT 59.288 36.000 0.00 0.00 33.36 2.12
4867 5259 6.032094 GCAACATTCCTGTCAAATCAGTATG 58.968 40.000 0.00 0.00 33.36 2.39
4868 5260 6.558009 CAACATTCCTGTCAAATCAGTATGG 58.442 40.000 0.00 0.00 33.36 2.74
4869 5261 5.195940 ACATTCCTGTCAAATCAGTATGGG 58.804 41.667 0.00 0.00 36.16 4.00
4870 5262 5.044919 ACATTCCTGTCAAATCAGTATGGGA 60.045 40.000 0.00 0.00 36.16 4.37
4871 5263 4.760530 TCCTGTCAAATCAGTATGGGAG 57.239 45.455 0.00 0.00 36.16 4.30
4872 5264 4.104086 TCCTGTCAAATCAGTATGGGAGT 58.896 43.478 0.00 0.00 36.16 3.85
4873 5265 4.536090 TCCTGTCAAATCAGTATGGGAGTT 59.464 41.667 0.00 0.00 36.16 3.01
4874 5266 4.878397 CCTGTCAAATCAGTATGGGAGTTC 59.122 45.833 0.00 0.00 36.16 3.01
4875 5267 5.338708 CCTGTCAAATCAGTATGGGAGTTCT 60.339 44.000 0.00 0.00 36.16 3.01
4876 5268 6.127054 CCTGTCAAATCAGTATGGGAGTTCTA 60.127 42.308 0.00 0.00 36.16 2.10
4877 5269 6.878317 TGTCAAATCAGTATGGGAGTTCTAG 58.122 40.000 0.00 0.00 36.16 2.43
4878 5270 6.440647 TGTCAAATCAGTATGGGAGTTCTAGT 59.559 38.462 0.00 0.00 36.16 2.57
4879 5271 7.038302 TGTCAAATCAGTATGGGAGTTCTAGTT 60.038 37.037 0.00 0.00 36.16 2.24
4880 5272 8.475639 GTCAAATCAGTATGGGAGTTCTAGTTA 58.524 37.037 0.00 0.00 36.16 2.24
4881 5273 9.042450 TCAAATCAGTATGGGAGTTCTAGTTAA 57.958 33.333 0.00 0.00 36.16 2.01
4882 5274 9.099454 CAAATCAGTATGGGAGTTCTAGTTAAC 57.901 37.037 0.00 0.00 36.16 2.01
4883 5275 7.973048 ATCAGTATGGGAGTTCTAGTTAACA 57.027 36.000 8.61 0.00 36.16 2.41
4884 5276 7.786046 TCAGTATGGGAGTTCTAGTTAACAA 57.214 36.000 8.61 0.00 36.16 2.83
4885 5277 8.197592 TCAGTATGGGAGTTCTAGTTAACAAA 57.802 34.615 8.61 0.00 36.16 2.83
4886 5278 8.092687 TCAGTATGGGAGTTCTAGTTAACAAAC 58.907 37.037 8.61 9.05 36.16 2.93
4887 5279 7.063074 CAGTATGGGAGTTCTAGTTAACAAACG 59.937 40.741 8.61 0.00 0.00 3.60
4888 5280 4.634199 TGGGAGTTCTAGTTAACAAACGG 58.366 43.478 8.61 0.00 0.00 4.44
4889 5281 4.101430 TGGGAGTTCTAGTTAACAAACGGT 59.899 41.667 8.61 0.00 0.00 4.83
4890 5282 4.450080 GGGAGTTCTAGTTAACAAACGGTG 59.550 45.833 8.61 0.00 0.00 4.94
4891 5283 4.084171 GGAGTTCTAGTTAACAAACGGTGC 60.084 45.833 8.61 2.98 0.00 5.01
4892 5284 4.444536 AGTTCTAGTTAACAAACGGTGCA 58.555 39.130 8.61 0.00 0.00 4.57
4893 5285 4.510340 AGTTCTAGTTAACAAACGGTGCAG 59.490 41.667 8.61 0.00 0.00 4.41
4894 5286 4.325028 TCTAGTTAACAAACGGTGCAGA 57.675 40.909 8.61 0.00 0.00 4.26
4895 5287 4.053295 TCTAGTTAACAAACGGTGCAGAC 58.947 43.478 8.61 0.00 0.00 3.51
4896 5288 1.595794 AGTTAACAAACGGTGCAGACG 59.404 47.619 8.61 9.00 37.36 4.18
4898 5290 0.931702 TAACAAACGGTGCAGACGTG 59.068 50.000 16.02 8.14 44.83 4.49
4908 5300 3.578456 CAGACGTGCATTGGTCCC 58.422 61.111 0.00 0.00 33.66 4.46
4909 5301 1.003355 CAGACGTGCATTGGTCCCT 60.003 57.895 0.00 0.00 33.66 4.20
4925 5317 0.984230 CCCTGTATGTCAGTGGGTGT 59.016 55.000 0.00 0.00 42.19 4.16
4955 5347 4.552365 TGCTCCGGCCAGCTATGC 62.552 66.667 15.52 5.12 40.39 3.14
4963 5355 2.903855 CCAGCTATGCGCCTTGGG 60.904 66.667 4.18 0.00 40.39 4.12
5075 5467 1.485480 GGTCCTCCTGTAAACCTAGCC 59.515 57.143 0.00 0.00 0.00 3.93
5076 5468 1.136500 GTCCTCCTGTAAACCTAGCCG 59.864 57.143 0.00 0.00 0.00 5.52
5077 5469 0.179081 CCTCCTGTAAACCTAGCCGC 60.179 60.000 0.00 0.00 0.00 6.53
5082 5474 3.392243 TAAACCTAGCCGCCGCCA 61.392 61.111 0.00 0.00 34.57 5.69
5180 5573 8.515695 TCTACGAGTGGAGTTCTCAATAATAA 57.484 34.615 0.00 0.00 32.79 1.40
5207 5600 6.762333 GTGTTTTCACTAGGTAGGTTTAGGA 58.238 40.000 0.00 0.00 46.30 2.94
5222 5615 4.333649 GGTTTAGGATTTTGGTAGCCGTAC 59.666 45.833 0.00 0.00 0.00 3.67
5234 5627 4.808649 CCGTACTCTTCTTCGGCC 57.191 61.111 0.00 0.00 36.68 6.13
5236 5629 0.179134 CCGTACTCTTCTTCGGCCAG 60.179 60.000 2.24 0.00 36.68 4.85
5237 5630 0.526662 CGTACTCTTCTTCGGCCAGT 59.473 55.000 2.24 0.00 0.00 4.00
5241 5664 1.071605 CTCTTCTTCGGCCAGTTTCG 58.928 55.000 2.24 0.00 0.00 3.46
5245 5668 0.105224 TCTTCGGCCAGTTTCGTTCA 59.895 50.000 2.24 0.00 0.00 3.18
5246 5669 0.512952 CTTCGGCCAGTTTCGTTCAG 59.487 55.000 2.24 0.00 0.00 3.02
5247 5670 0.179067 TTCGGCCAGTTTCGTTCAGT 60.179 50.000 2.24 0.00 0.00 3.41
5248 5671 0.878523 TCGGCCAGTTTCGTTCAGTG 60.879 55.000 2.24 0.00 0.00 3.66
5259 5682 1.738350 TCGTTCAGTGACGAGATCTCC 59.262 52.381 17.13 4.63 46.09 3.71
5261 5684 2.162608 CGTTCAGTGACGAGATCTCCTT 59.837 50.000 17.13 4.12 45.47 3.36
5264 5687 2.025793 TCAGTGACGAGATCTCCTTCCT 60.026 50.000 17.13 9.72 0.00 3.36
5265 5688 2.098934 CAGTGACGAGATCTCCTTCCTG 59.901 54.545 17.13 16.07 0.00 3.86
5266 5689 1.407258 GTGACGAGATCTCCTTCCTGG 59.593 57.143 17.13 3.70 37.10 4.45
5267 5690 1.006043 TGACGAGATCTCCTTCCTGGT 59.994 52.381 17.13 6.99 37.07 4.00
5291 5714 4.039124 GTCAATGGTGGTGTTGGAAGATTT 59.961 41.667 0.00 0.00 0.00 2.17
5292 5715 4.653341 TCAATGGTGGTGTTGGAAGATTTT 59.347 37.500 0.00 0.00 0.00 1.82
5293 5716 4.605640 ATGGTGGTGTTGGAAGATTTTG 57.394 40.909 0.00 0.00 0.00 2.44
5294 5717 2.697751 TGGTGGTGTTGGAAGATTTTGG 59.302 45.455 0.00 0.00 0.00 3.28
5295 5718 2.962421 GGTGGTGTTGGAAGATTTTGGA 59.038 45.455 0.00 0.00 0.00 3.53
5325 5802 3.251484 TCTTGGTCAAGGAGGATTGTCT 58.749 45.455 10.39 0.00 38.88 3.41
5326 5803 4.425772 TCTTGGTCAAGGAGGATTGTCTA 58.574 43.478 10.39 0.00 38.88 2.59
5340 5817 5.303078 AGGATTGTCTACGCAATATCTGTCT 59.697 40.000 0.00 0.00 38.98 3.41
5343 5820 3.003378 TGTCTACGCAATATCTGTCTCGG 59.997 47.826 0.00 0.00 0.00 4.63
5356 5833 1.677966 TCTCGGCTGCTACGTCCTT 60.678 57.895 0.00 0.00 0.00 3.36
5364 5841 2.930887 GCTGCTACGTCCTTGACAATGA 60.931 50.000 0.00 0.00 32.09 2.57
5436 5914 4.588899 TGTCCCTGAAATACTGATGTTGG 58.411 43.478 0.00 0.00 0.00 3.77
5448 5926 3.005554 CTGATGTTGGTACTCTTGCTGG 58.994 50.000 0.00 0.00 0.00 4.85
5461 5939 3.030291 TCTTGCTGGTGTTGGTTGATTT 58.970 40.909 0.00 0.00 0.00 2.17
5465 5943 4.211125 TGCTGGTGTTGGTTGATTTCTTA 58.789 39.130 0.00 0.00 0.00 2.10
5470 5948 6.520272 TGGTGTTGGTTGATTTCTTAAATGG 58.480 36.000 0.00 0.00 0.00 3.16
5471 5949 5.408299 GGTGTTGGTTGATTTCTTAAATGGC 59.592 40.000 0.00 0.00 0.00 4.40
5472 5950 6.223120 GTGTTGGTTGATTTCTTAAATGGCT 58.777 36.000 0.00 0.00 0.00 4.75
5473 5951 6.146021 GTGTTGGTTGATTTCTTAAATGGCTG 59.854 38.462 0.00 0.00 0.00 4.85
5487 5965 4.170062 GCTGCGTGCGTGCATCAT 62.170 61.111 2.93 0.00 45.26 2.45
5494 5972 0.028505 GTGCGTGCATCATAGCCTTG 59.971 55.000 0.00 0.00 0.00 3.61
5497 5975 0.816825 CGTGCATCATAGCCTTGGCT 60.817 55.000 18.74 18.74 0.00 4.75
5510 5988 0.940991 CTTGGCTTTGCGGCTCAAAC 60.941 55.000 0.00 0.00 39.58 2.93
5516 5994 2.726241 GCTTTGCGGCTCAAACTAAAAG 59.274 45.455 0.00 1.25 39.58 2.27
5517 5995 3.308530 CTTTGCGGCTCAAACTAAAAGG 58.691 45.455 0.00 0.00 39.58 3.11
5518 5996 1.243902 TGCGGCTCAAACTAAAAGGG 58.756 50.000 0.00 0.00 0.00 3.95
5522 6000 2.812613 CGGCTCAAACTAAAAGGGTGGA 60.813 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.227409 ACCATTGACACGCACGTCA 60.227 52.632 1.18 1.18 44.05 4.35
89 90 1.266446 TCACCGTTCACATGCACATTG 59.734 47.619 0.00 0.00 0.00 2.82
91 92 1.469703 CATCACCGTTCACATGCACAT 59.530 47.619 0.00 0.00 0.00 3.21
128 129 1.066286 TCATCACCATCGACATGCACA 60.066 47.619 0.00 0.00 0.00 4.57
156 157 3.257873 CCCCTTTTGCATGACAACATACA 59.742 43.478 0.00 0.00 38.23 2.29
170 171 4.270008 CTTGTACCACCTATCCCCTTTTG 58.730 47.826 0.00 0.00 0.00 2.44
172 173 2.850568 CCTTGTACCACCTATCCCCTTT 59.149 50.000 0.00 0.00 0.00 3.11
180 181 4.684724 AGTTCTGATCCTTGTACCACCTA 58.315 43.478 0.00 0.00 0.00 3.08
183 184 8.204836 ACATTATAGTTCTGATCCTTGTACCAC 58.795 37.037 0.00 0.00 0.00 4.16
198 199 5.861787 GGGTTTGTTGCACACATTATAGTTC 59.138 40.000 0.00 0.00 34.43 3.01
226 227 4.700268 TGTATTAGAGCGGTCGTTTGTA 57.300 40.909 9.28 0.00 0.00 2.41
229 230 3.131577 TCCATGTATTAGAGCGGTCGTTT 59.868 43.478 9.28 0.26 0.00 3.60
237 238 9.712305 ATTATTGTACAGTCCATGTATTAGAGC 57.288 33.333 0.00 0.00 45.94 4.09
249 250 8.072567 GCAATGATCTTCATTATTGTACAGTCC 58.927 37.037 0.00 0.00 44.60 3.85
274 275 0.878523 TGTGCGGTACTGTGTTGAGC 60.879 55.000 3.10 0.00 0.00 4.26
275 276 1.577468 TTGTGCGGTACTGTGTTGAG 58.423 50.000 3.10 0.00 0.00 3.02
277 278 3.322369 TCTATTGTGCGGTACTGTGTTG 58.678 45.455 3.10 0.00 0.00 3.33
289 291 3.381590 GGGGAAGGTCATTTCTATTGTGC 59.618 47.826 0.00 0.00 0.00 4.57
292 294 6.608808 AGATTTGGGGAAGGTCATTTCTATTG 59.391 38.462 0.00 0.00 0.00 1.90
328 330 2.613506 GGGCTCGTTTTGGGTGTCG 61.614 63.158 0.00 0.00 0.00 4.35
333 335 0.177141 TCGATAGGGCTCGTTTTGGG 59.823 55.000 0.00 0.00 39.62 4.12
341 343 3.579151 AGATTTAGGGTTCGATAGGGCTC 59.421 47.826 0.00 0.00 0.00 4.70
350 352 5.883673 TGATTTGGGTTAGATTTAGGGTTCG 59.116 40.000 0.00 0.00 0.00 3.95
399 401 5.010719 TGAAGTAATACTGATCTAAGGCCCG 59.989 44.000 0.00 0.00 0.00 6.13
400 402 6.224584 GTGAAGTAATACTGATCTAAGGCCC 58.775 44.000 0.00 0.00 0.00 5.80
404 406 9.535878 GGAAAGGTGAAGTAATACTGATCTAAG 57.464 37.037 0.00 0.00 0.00 2.18
411 413 5.880887 GGGAAGGAAAGGTGAAGTAATACTG 59.119 44.000 0.00 0.00 0.00 2.74
412 414 5.045066 GGGGAAGGAAAGGTGAAGTAATACT 60.045 44.000 0.00 0.00 0.00 2.12
417 419 2.374170 GTGGGGAAGGAAAGGTGAAGTA 59.626 50.000 0.00 0.00 0.00 2.24
441 444 3.744942 GGATGATGGACTCAATGATGTCG 59.255 47.826 6.71 0.00 37.44 4.35
450 453 1.008815 ACCTCAGGGATGATGGACTCA 59.991 52.381 0.00 0.00 35.56 3.41
466 469 1.967319 TGTTGAAGCACTTGGACCTC 58.033 50.000 0.00 0.00 0.00 3.85
484 487 2.626743 GGATGGCAATTTGGAGGAGATG 59.373 50.000 0.00 0.00 0.00 2.90
516 519 3.399330 TCAAGTGAAATCCTGGTTCGTC 58.601 45.455 0.00 0.00 0.00 4.20
517 520 3.403038 CTCAAGTGAAATCCTGGTTCGT 58.597 45.455 0.00 0.00 0.00 3.85
531 534 3.743396 GTGGTCTTGTAGAAGCTCAAGTG 59.257 47.826 11.43 0.00 40.97 3.16
532 535 3.388024 TGTGGTCTTGTAGAAGCTCAAGT 59.612 43.478 11.43 0.00 40.97 3.16
533 536 3.743396 GTGTGGTCTTGTAGAAGCTCAAG 59.257 47.826 6.56 6.56 41.36 3.02
534 537 3.388024 AGTGTGGTCTTGTAGAAGCTCAA 59.612 43.478 0.00 0.00 0.00 3.02
536 539 3.321497 CAGTGTGGTCTTGTAGAAGCTC 58.679 50.000 0.00 0.00 0.00 4.09
537 540 2.548920 GCAGTGTGGTCTTGTAGAAGCT 60.549 50.000 0.00 0.00 0.00 3.74
538 541 1.801178 GCAGTGTGGTCTTGTAGAAGC 59.199 52.381 0.00 0.00 0.00 3.86
539 542 2.417719 GGCAGTGTGGTCTTGTAGAAG 58.582 52.381 0.00 0.00 0.00 2.85
585 589 6.363626 CAGCACGAGTTCCATGTTATATCTAC 59.636 42.308 0.00 0.00 0.00 2.59
701 705 9.305925 GATTCGGAAATAGAAAATCTGCATTTT 57.694 29.630 0.00 0.00 43.64 1.82
702 706 8.469200 TGATTCGGAAATAGAAAATCTGCATTT 58.531 29.630 0.00 0.00 33.27 2.32
704 708 7.572523 TGATTCGGAAATAGAAAATCTGCAT 57.427 32.000 0.00 0.00 0.00 3.96
706 710 8.862550 AAATGATTCGGAAATAGAAAATCTGC 57.137 30.769 0.00 0.00 0.00 4.26
710 714 9.927668 ACACAAAATGATTCGGAAATAGAAAAT 57.072 25.926 0.00 0.00 0.00 1.82
720 751 3.331150 ACGCTACACAAAATGATTCGGA 58.669 40.909 0.00 0.00 0.00 4.55
845 881 1.342076 GGGGGCTTAAAAAGGGAGGAG 60.342 57.143 0.00 0.00 0.00 3.69
846 882 0.708209 GGGGGCTTAAAAAGGGAGGA 59.292 55.000 0.00 0.00 0.00 3.71
847 883 0.411848 TGGGGGCTTAAAAAGGGAGG 59.588 55.000 0.00 0.00 0.00 4.30
848 884 1.357761 TCTGGGGGCTTAAAAAGGGAG 59.642 52.381 0.00 0.00 0.00 4.30
849 885 1.357761 CTCTGGGGGCTTAAAAAGGGA 59.642 52.381 0.00 0.00 0.00 4.20
973 1012 5.090139 GAGGGATTGATAGATTCAGGAGGA 58.910 45.833 0.00 0.00 35.27 3.71
1031 1076 3.021695 GCCCCAGAAAAGGTATTGGTAC 58.978 50.000 0.00 0.00 0.00 3.34
1196 1241 7.093289 TGACCTTCAGAAAGTAAATAGAGGAGG 60.093 40.741 0.00 0.00 0.00 4.30
1213 1260 5.649557 TGTCAAACAAAACATGACCTTCAG 58.350 37.500 0.00 0.00 42.12 3.02
1232 1288 4.908601 AAACATGACCCTGATACTGTCA 57.091 40.909 0.00 0.00 42.65 3.58
1269 1325 8.762481 ACCTTATTTTAATAACCCTGTGATCC 57.238 34.615 0.00 0.00 0.00 3.36
1296 1352 6.150396 AGGTACTCATCTAATTCGAACCAG 57.850 41.667 0.00 0.11 0.00 4.00
1535 1602 7.886629 TGCTCAAATTAAGATAGGCTCAAAT 57.113 32.000 0.00 0.00 0.00 2.32
1588 1956 3.788227 ATACTTGTTGGAAGGACAGCA 57.212 42.857 0.00 0.00 0.00 4.41
1604 1972 3.492102 AGTATCATGCCCGCAAATACT 57.508 42.857 16.43 16.43 35.77 2.12
1623 1991 8.040132 TGGCCTGAAAACCATCATAAAAATTAG 58.960 33.333 3.32 0.00 0.00 1.73
1660 2028 0.036483 TCCTTGTAGCAGCATCGCAA 60.036 50.000 0.00 0.00 0.00 4.85
1855 2223 4.064768 TCCCCTGCATTGCCCCTG 62.065 66.667 6.12 0.00 0.00 4.45
1901 2269 2.297701 AGTGAAACAAGTGGCACGATT 58.702 42.857 12.71 5.12 41.43 3.34
1944 2312 5.224821 AGTTACAAGGTCAGGAGTAAACC 57.775 43.478 0.00 0.00 0.00 3.27
2179 2549 7.661040 AGCATATGTGTATAAAAGAAATGCCC 58.339 34.615 4.29 0.00 0.00 5.36
2287 2657 7.566760 TCTTAGTCATGAACAACAAATGTGT 57.433 32.000 0.00 0.00 42.99 3.72
2602 2972 4.771590 AATGGCATGCCTAATATCAACG 57.228 40.909 35.53 0.00 36.94 4.10
2664 3034 2.158856 TCTAACGATCTACCTCGCTCCA 60.159 50.000 0.00 0.00 42.35 3.86
2669 3039 5.501092 CGCATCTATCTAACGATCTACCTCG 60.501 48.000 0.00 0.00 44.14 4.63
2672 3042 5.798015 TCGCATCTATCTAACGATCTACC 57.202 43.478 0.00 0.00 0.00 3.18
2679 3049 7.591795 ACAGAATTACTTCGCATCTATCTAACG 59.408 37.037 0.00 0.00 36.45 3.18
2683 3053 7.078851 CGTACAGAATTACTTCGCATCTATCT 58.921 38.462 0.00 0.00 36.45 1.98
2685 3055 6.637254 CACGTACAGAATTACTTCGCATCTAT 59.363 38.462 0.00 0.00 36.45 1.98
2808 3179 8.335356 CCTAATATCAACGTCAACATTAACCAG 58.665 37.037 0.00 0.00 0.00 4.00
2816 3187 4.035091 GCATGCCTAATATCAACGTCAACA 59.965 41.667 6.36 0.00 0.00 3.33
3073 3444 6.161170 ACTGGGATGGAAATTTAAGGAGATCT 59.839 38.462 0.00 0.00 0.00 2.75
3202 3573 3.682696 AGAATCAGCAATCTTGTCAGCA 58.317 40.909 0.00 0.00 0.00 4.41
3997 4368 6.582295 GCCAACATAATTGATATAAACCTGCG 59.418 38.462 0.00 0.00 0.00 5.18
4109 4480 5.832539 AGCATGGTATGGTAAGATAAGCT 57.167 39.130 0.00 0.00 39.58 3.74
4232 4603 8.511604 ACTCAAAGCATATACAAAACAGCTAT 57.488 30.769 0.00 0.00 0.00 2.97
4233 4604 7.606073 TGACTCAAAGCATATACAAAACAGCTA 59.394 33.333 0.00 0.00 0.00 3.32
4234 4605 6.430925 TGACTCAAAGCATATACAAAACAGCT 59.569 34.615 0.00 0.00 0.00 4.24
4309 4680 2.566708 AGCCTCCTCTTCTCTCCAAT 57.433 50.000 0.00 0.00 0.00 3.16
4421 4795 0.106769 TGTGGTCCAAAAGCAGAGCA 60.107 50.000 0.00 0.00 38.12 4.26
4454 4828 3.892588 ACAACCGATTTACCACCATTGTT 59.107 39.130 0.00 0.00 0.00 2.83
4544 4919 2.678336 GCATAAAACAGGAACGAGAGGG 59.322 50.000 0.00 0.00 0.00 4.30
4546 4921 2.348666 CGGCATAAAACAGGAACGAGAG 59.651 50.000 0.00 0.00 0.00 3.20
4615 4990 3.376859 CACATAGCCTATGCGGAACAAAA 59.623 43.478 11.65 0.00 44.33 2.44
4825 5217 5.069318 TGTTGCATTGACAGGAACAAGATA 58.931 37.500 0.00 0.00 42.95 1.98
4840 5232 5.011329 ACTGATTTGACAGGAATGTTGCATT 59.989 36.000 0.00 0.00 41.59 3.56
4859 5251 7.973048 TGTTAACTAGAACTCCCATACTGAT 57.027 36.000 7.22 0.00 0.00 2.90
4862 5254 7.095270 CGTTTGTTAACTAGAACTCCCATACT 58.905 38.462 7.22 0.00 31.89 2.12
4865 5257 5.221783 ACCGTTTGTTAACTAGAACTCCCAT 60.222 40.000 7.22 0.00 31.89 4.00
4866 5258 4.101430 ACCGTTTGTTAACTAGAACTCCCA 59.899 41.667 7.22 0.00 31.89 4.37
4867 5259 4.450080 CACCGTTTGTTAACTAGAACTCCC 59.550 45.833 7.22 0.00 31.89 4.30
4868 5260 4.084171 GCACCGTTTGTTAACTAGAACTCC 60.084 45.833 7.22 0.00 31.89 3.85
4869 5261 4.508861 TGCACCGTTTGTTAACTAGAACTC 59.491 41.667 7.22 1.35 31.89 3.01
4870 5262 4.444536 TGCACCGTTTGTTAACTAGAACT 58.555 39.130 7.22 0.00 31.89 3.01
4871 5263 4.508861 TCTGCACCGTTTGTTAACTAGAAC 59.491 41.667 7.22 8.25 31.89 3.01
4872 5264 4.508861 GTCTGCACCGTTTGTTAACTAGAA 59.491 41.667 7.22 0.00 31.89 2.10
4873 5265 4.053295 GTCTGCACCGTTTGTTAACTAGA 58.947 43.478 7.22 0.00 31.89 2.43
4874 5266 3.121126 CGTCTGCACCGTTTGTTAACTAG 60.121 47.826 7.22 0.00 31.89 2.57
4875 5267 2.796031 CGTCTGCACCGTTTGTTAACTA 59.204 45.455 7.22 0.00 31.89 2.24
4876 5268 1.595794 CGTCTGCACCGTTTGTTAACT 59.404 47.619 7.22 0.00 31.89 2.24
4877 5269 1.328374 ACGTCTGCACCGTTTGTTAAC 59.672 47.619 0.00 0.00 34.28 2.01
4878 5270 1.328069 CACGTCTGCACCGTTTGTTAA 59.672 47.619 4.03 0.00 36.17 2.01
4879 5271 0.931702 CACGTCTGCACCGTTTGTTA 59.068 50.000 4.03 0.00 36.17 2.41
4880 5272 1.719117 CACGTCTGCACCGTTTGTT 59.281 52.632 4.03 0.00 36.17 2.83
4881 5273 2.819552 GCACGTCTGCACCGTTTGT 61.820 57.895 4.03 0.00 43.62 2.83
4882 5274 2.052237 GCACGTCTGCACCGTTTG 60.052 61.111 4.03 0.00 43.62 2.93
4890 5282 2.690778 GGGACCAATGCACGTCTGC 61.691 63.158 9.53 0.00 44.52 4.26
4891 5283 1.003355 AGGGACCAATGCACGTCTG 60.003 57.895 9.53 0.00 0.00 3.51
4892 5284 1.003355 CAGGGACCAATGCACGTCT 60.003 57.895 9.53 0.00 0.00 4.18
4893 5285 0.036765 TACAGGGACCAATGCACGTC 60.037 55.000 0.00 0.00 0.00 4.34
4894 5286 0.618458 ATACAGGGACCAATGCACGT 59.382 50.000 0.00 0.00 0.00 4.49
4895 5287 1.016627 CATACAGGGACCAATGCACG 58.983 55.000 0.00 0.00 0.00 5.34
4896 5288 2.017049 GACATACAGGGACCAATGCAC 58.983 52.381 0.00 0.00 0.00 4.57
4897 5289 1.632920 TGACATACAGGGACCAATGCA 59.367 47.619 0.00 0.00 0.00 3.96
4898 5290 2.292267 CTGACATACAGGGACCAATGC 58.708 52.381 0.00 0.00 42.39 3.56
4907 5299 5.101139 GGTTTACACCCACTGACATACAGG 61.101 50.000 0.00 0.00 42.95 4.00
4908 5300 4.000988 GGTTTACACCCACTGACATACAG 58.999 47.826 0.00 0.00 43.64 2.74
4909 5301 3.555377 CGGTTTACACCCACTGACATACA 60.555 47.826 0.00 0.00 40.52 2.29
4959 5351 1.456705 AGAACCGGCAAAAGCCCAA 60.457 52.632 0.00 0.00 0.00 4.12
5034 5426 1.548719 TCTCGAGCGAGGGAATGAAAA 59.451 47.619 18.57 0.00 42.20 2.29
5059 5451 0.179081 GGCGGCTAGGTTTACAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
5082 5474 1.481428 CCGATCTATGGTGGAGGAGGT 60.481 57.143 0.00 0.00 0.00 3.85
5085 5477 2.317040 GAACCGATCTATGGTGGAGGA 58.683 52.381 0.00 0.00 40.35 3.71
5180 5573 8.537858 CCTAAACCTACCTAGTGAAAACACTAT 58.462 37.037 9.91 0.97 37.09 2.12
5196 5589 4.573607 CGGCTACCAAAATCCTAAACCTAC 59.426 45.833 0.00 0.00 0.00 3.18
5207 5600 4.820894 AGAAGAGTACGGCTACCAAAAT 57.179 40.909 0.00 0.00 0.00 1.82
5222 5615 1.071605 CGAAACTGGCCGAAGAAGAG 58.928 55.000 0.00 0.00 0.00 2.85
5241 5664 3.428316 GGAAGGAGATCTCGTCACTGAAC 60.428 52.174 17.78 0.35 0.00 3.18
5245 5668 2.374184 CAGGAAGGAGATCTCGTCACT 58.626 52.381 17.78 15.10 0.00 3.41
5246 5669 1.407258 CCAGGAAGGAGATCTCGTCAC 59.593 57.143 17.78 13.29 41.22 3.67
5247 5670 1.006043 ACCAGGAAGGAGATCTCGTCA 59.994 52.381 17.78 0.00 41.22 4.35
5248 5671 1.407258 CACCAGGAAGGAGATCTCGTC 59.593 57.143 17.78 15.65 41.22 4.20
5258 5681 1.538047 CACCATTGACACCAGGAAGG 58.462 55.000 0.00 0.00 45.67 3.46
5259 5682 1.202927 ACCACCATTGACACCAGGAAG 60.203 52.381 0.00 0.00 0.00 3.46
5261 5684 0.110295 CACCACCATTGACACCAGGA 59.890 55.000 0.00 0.00 0.00 3.86
5264 5687 1.397672 CAACACCACCATTGACACCA 58.602 50.000 0.00 0.00 0.00 4.17
5265 5688 0.673437 CCAACACCACCATTGACACC 59.327 55.000 0.00 0.00 0.00 4.16
5266 5689 1.686355 TCCAACACCACCATTGACAC 58.314 50.000 0.00 0.00 0.00 3.67
5267 5690 2.092158 TCTTCCAACACCACCATTGACA 60.092 45.455 0.00 0.00 0.00 3.58
5306 5778 3.056107 CGTAGACAATCCTCCTTGACCAA 60.056 47.826 0.00 0.00 0.00 3.67
5312 5784 3.914426 ATTGCGTAGACAATCCTCCTT 57.086 42.857 0.00 0.00 35.31 3.36
5325 5802 1.954382 AGCCGAGACAGATATTGCGTA 59.046 47.619 0.00 0.00 0.00 4.42
5326 5803 0.747255 AGCCGAGACAGATATTGCGT 59.253 50.000 0.00 0.00 0.00 5.24
5340 5817 1.974875 TCAAGGACGTAGCAGCCGA 60.975 57.895 0.00 0.00 0.00 5.54
5343 5820 1.394917 CATTGTCAAGGACGTAGCAGC 59.605 52.381 0.00 0.00 34.95 5.25
5356 5833 6.218746 CCGAGAGTATGAATCATCATTGTCA 58.781 40.000 0.00 0.00 43.89 3.58
5364 5841 2.564947 GGGAGCCGAGAGTATGAATCAT 59.435 50.000 0.00 0.00 0.00 2.45
5386 5863 2.432628 CAACCAGGTCGAGTCGCC 60.433 66.667 7.92 12.55 0.00 5.54
5422 5900 6.372659 CAGCAAGAGTACCAACATCAGTATTT 59.627 38.462 0.00 0.00 0.00 1.40
5430 5908 2.106511 ACACCAGCAAGAGTACCAACAT 59.893 45.455 0.00 0.00 0.00 2.71
5436 5914 2.256117 ACCAACACCAGCAAGAGTAC 57.744 50.000 0.00 0.00 0.00 2.73
5448 5926 6.146021 CAGCCATTTAAGAAATCAACCAACAC 59.854 38.462 0.00 0.00 0.00 3.32
5461 5939 0.953471 ACGCACGCAGCCATTTAAGA 60.953 50.000 0.00 0.00 41.38 2.10
5465 5943 4.705519 GCACGCACGCAGCCATTT 62.706 61.111 0.00 0.00 41.38 2.32
5470 5948 2.691107 CTATGATGCACGCACGCAGC 62.691 60.000 5.69 5.69 46.99 5.25
5471 5949 1.274770 CTATGATGCACGCACGCAG 59.725 57.895 3.23 0.00 46.99 5.18
5473 5951 2.052766 GCTATGATGCACGCACGC 60.053 61.111 0.00 0.00 0.00 5.34
5494 5972 0.596082 TTAGTTTGAGCCGCAAAGCC 59.404 50.000 0.00 0.00 46.48 4.35
5497 5975 2.035321 CCCTTTTAGTTTGAGCCGCAAA 59.965 45.455 0.00 0.00 43.89 3.68


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

AutoCloner maintained by Alex Coulton.