Multiple sequence alignment - TraesCS7D01G387100

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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 TraesCS7D01G387100 chr7D 100.000 5368 0 0 1 5368 501087603 501092970 0.000000e+00 9913.0
1 TraesCS7D01G387100 chr7A 95.412 3814 135 22 794 4572 567576361 567580169 0.000000e+00 6037.0
2 TraesCS7D01G387100 chr7A 90.654 428 24 10 385 801 567575889 567576311 6.070000e-154 555.0
3 TraesCS7D01G387100 chr7A 88.498 426 30 14 1 409 567575419 567575842 1.040000e-136 497.0
4 TraesCS7D01G387100 chr7A 90.616 341 21 6 5031 5368 567580823 567581155 4.930000e-120 442.0
5 TraesCS7D01G387100 chr7B 93.263 4097 196 33 807 4869 530372785 530376835 0.000000e+00 5963.0
6 TraesCS7D01G387100 chr7B 91.740 339 22 3 5031 5368 530376834 530377167 2.930000e-127 466.0
7 TraesCS7D01G387100 chr7B 85.167 418 42 13 1 409 530364332 530364738 1.390000e-110 411.0
8 TraesCS7D01G387100 chr5B 79.890 910 122 33 2899 3777 580105700 580104821 1.280000e-170 610.0
9 TraesCS7D01G387100 chr5B 80.261 537 66 15 2341 2838 580106543 580106008 8.490000e-98 368.0
10 TraesCS7D01G387100 chr5A 81.287 513 56 16 2363 2838 592296283 592295774 3.920000e-101 379.0
11 TraesCS7D01G387100 chr5A 87.647 170 16 2 3613 3777 592294778 592294609 5.490000e-45 193.0
12 TraesCS7D01G387100 chr5A 82.258 186 28 3 4514 4694 537659909 537660094 7.200000e-34 156.0
13 TraesCS7D01G387100 chr5D 77.875 574 73 26 2166 2733 472741126 472740601 1.880000e-79 307.0
14 TraesCS7D01G387100 chr5D 90.860 186 13 4 4865 5047 445106484 445106668 4.150000e-61 246.0
15 TraesCS7D01G387100 chr5D 88.889 171 14 2 3613 3778 472739275 472739105 7.050000e-49 206.0
16 TraesCS7D01G387100 chr6B 93.678 174 11 0 4868 5041 118037253 118037080 1.480000e-65 261.0
17 TraesCS7D01G387100 chr6B 93.642 173 11 0 4864 5036 27810912 27811084 5.330000e-65 259.0
18 TraesCS7D01G387100 chr6B 93.064 173 11 1 4866 5037 25248001 25247829 8.930000e-63 252.0
19 TraesCS7D01G387100 chr6B 92.529 174 13 0 4864 5037 175326151 175325978 3.210000e-62 250.0
20 TraesCS7D01G387100 chr6B 92.308 52 2 2 527 578 715719619 715719570 7.460000e-09 73.1
21 TraesCS7D01G387100 chr3A 92.737 179 13 0 4857 5035 662422520 662422342 5.330000e-65 259.0
22 TraesCS7D01G387100 chr3A 81.106 217 29 7 4517 4725 593345203 593344991 4.300000e-36 163.0
23 TraesCS7D01G387100 chr3A 80.288 208 34 4 4514 4716 439405212 439405417 3.350000e-32 150.0
24 TraesCS7D01G387100 chr3A 91.111 45 4 0 527 571 17431501 17431457 1.610000e-05 62.1
25 TraesCS7D01G387100 chr4D 93.567 171 11 0 4867 5037 93336683 93336853 6.900000e-64 255.0
26 TraesCS7D01G387100 chr4D 79.832 119 21 2 540 656 464084290 464084407 3.450000e-12 84.2
27 TraesCS7D01G387100 chr2D 93.023 172 12 0 4866 5037 609886789 609886960 8.930000e-63 252.0
28 TraesCS7D01G387100 chr2D 100.000 30 0 0 1145 1174 55059626 55059597 7.510000e-04 56.5
29 TraesCS7D01G387100 chr1D 92.571 175 12 1 4860 5034 68439335 68439162 3.210000e-62 250.0
30 TraesCS7D01G387100 chr3B 80.645 217 30 7 4517 4725 591369910 591369698 2.000000e-34 158.0
31 TraesCS7D01G387100 chr3B 82.353 187 27 4 4514 4695 740054981 740055166 2.000000e-34 158.0
32 TraesCS7D01G387100 chr6A 82.258 186 28 3 4514 4694 585169173 585169358 7.200000e-34 156.0
33 TraesCS7D01G387100 chr6A 80.000 205 33 5 4514 4713 597842670 597842871 1.560000e-30 145.0
34 TraesCS7D01G387100 chr6A 78.378 222 39 6 4514 4729 131197124 131197342 9.380000e-28 135.0
35 TraesCS7D01G387100 chr1A 82.514 183 27 3 4517 4694 417384994 417385176 7.200000e-34 156.0
36 TraesCS7D01G387100 chr1A 82.258 186 28 3 4514 4694 578754423 578754608 7.200000e-34 156.0
37 TraesCS7D01G387100 chr1A 78.539 219 38 8 4517 4729 67985773 67985558 9.380000e-28 135.0
38 TraesCS7D01G387100 chr4A 78.829 222 38 6 4514 4729 518619476 518619694 2.020000e-29 141.0
39 TraesCS7D01G387100 chr4A 78.378 222 38 8 4514 4729 21147026 21147243 9.380000e-28 135.0
40 TraesCS7D01G387100 chr2A 79.426 209 36 4 4517 4721 468203491 468203286 2.020000e-29 141.0
41 TraesCS7D01G387100 chr3D 91.111 45 4 0 527 571 10900109 10900153 1.610000e-05 62.1


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 TraesCS7D01G387100 chr7D 501087603 501092970 5367 False 9913.00 9913 100.0000 1 5368 1 chr7D.!!$F1 5367
1 TraesCS7D01G387100 chr7A 567575419 567581155 5736 False 1882.75 6037 91.2950 1 5368 4 chr7A.!!$F1 5367
2 TraesCS7D01G387100 chr7B 530372785 530377167 4382 False 3214.50 5963 92.5015 807 5368 2 chr7B.!!$F2 4561
3 TraesCS7D01G387100 chr5B 580104821 580106543 1722 True 489.00 610 80.0755 2341 3777 2 chr5B.!!$R1 1436
4 TraesCS7D01G387100 chr5A 592294609 592296283 1674 True 286.00 379 84.4670 2363 3777 2 chr5A.!!$R1 1414
5 TraesCS7D01G387100 chr5D 472739105 472741126 2021 True 256.50 307 83.3820 2166 3778 2 chr5D.!!$R1 1612

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
28 29 0.668535 GTGCTTCACTTTGGGGTGAC 59.331 55.0 0.00 0.00 44.55 3.67 F
1315 1495 0.239613 CCGACGATGAGAGCGATGAT 59.760 55.0 0.00 0.00 0.00 2.45 F
2923 3498 2.105477 ACTGCATCCTTATACCCAGCTG 59.895 50.0 6.78 6.78 0.00 4.24 F
3969 4679 0.324943 TGGAGGAAGAAAGCGAAGGG 59.675 55.0 0.00 0.00 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1768 0.252239 TCTCTGCCTGCAACCTCCTA 60.252 55.000 0.00 0.0 0.00 2.94 R
3223 3880 1.002544 AGCTGGAAGACAAGTGTAGCC 59.997 52.381 0.00 0.0 34.07 3.93 R
4240 4950 0.675522 CCCCACGCGAACTAAACCAT 60.676 55.000 15.93 0.0 0.00 3.55 R
5157 6295 1.068748 GTTGACTGCAGGCACTTCATG 60.069 52.381 25.40 0.0 34.60 3.07 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
28 29 0.668535 GTGCTTCACTTTGGGGTGAC 59.331 55.000 0.00 0.00 44.55 3.67
43 44 3.192633 GGGGTGACGCACAAAAGAATAAT 59.807 43.478 11.20 0.00 43.99 1.28
53 54 7.167468 ACGCACAAAAGAATAATTGTCTTTCAC 59.833 33.333 15.42 7.86 43.00 3.18
252 278 3.597377 AACAGAAAACCGCGAAAGTAC 57.403 42.857 8.23 0.00 0.00 2.73
278 304 3.781341 CACAATTTGTGCTTCACATGC 57.219 42.857 16.05 0.00 44.16 4.06
526 639 9.122779 TCTGTTTTCCGGTTCTCTTTTATTTTA 57.877 29.630 0.00 0.00 0.00 1.52
527 640 9.738832 CTGTTTTCCGGTTCTCTTTTATTTTAA 57.261 29.630 0.00 0.00 0.00 1.52
638 751 6.653320 TGGACGCACAACTTAAGAGATAAAAT 59.347 34.615 10.09 0.00 0.00 1.82
672 786 8.593492 AAGAATGAAAATAAAAGCACAACCTC 57.407 30.769 0.00 0.00 0.00 3.85
855 1029 2.407026 GCGCTAACCAAAAACCGAAATG 59.593 45.455 0.00 0.00 0.00 2.32
925 1099 2.037049 ACGGCATGCCAATCCCAA 59.963 55.556 34.93 0.00 35.37 4.12
926 1100 2.350458 ACGGCATGCCAATCCCAAC 61.350 57.895 34.93 6.13 35.37 3.77
939 1113 1.438651 TCCCAACTCGCTTCATTTCG 58.561 50.000 0.00 0.00 0.00 3.46
1178 1358 2.181521 GCGATCTCCGACTCCGACT 61.182 63.158 0.00 0.00 41.76 4.18
1179 1359 1.935925 CGATCTCCGACTCCGACTC 59.064 63.158 0.00 0.00 41.76 3.36
1229 1409 2.036731 ACGTCATCCCCCTCGACA 59.963 61.111 0.00 0.00 0.00 4.35
1315 1495 0.239613 CCGACGATGAGAGCGATGAT 59.760 55.000 0.00 0.00 0.00 2.45
1588 1768 5.708697 TGATGATGTTGAGTTTGATGAGCTT 59.291 36.000 0.00 0.00 0.00 3.74
1671 1851 9.098355 TGAAAGTGATGAAGAGGATAATAAACG 57.902 33.333 0.00 0.00 0.00 3.60
2178 2358 4.964897 TCTAGAGAATGAGGGCAAATCTCA 59.035 41.667 0.00 0.00 44.19 3.27
2283 2472 4.039488 TGAAATTGCAAGCAAGGATGAGTT 59.961 37.500 13.35 0.00 39.47 3.01
2533 2724 8.725606 ACAAGGTATGGGATATTTTTATGCAT 57.274 30.769 3.79 3.79 0.00 3.96
2557 2748 7.972623 TGTTTCTTATTGTTGTTGGTTTACG 57.027 32.000 0.00 0.00 0.00 3.18
2723 2925 6.894654 TCTCATGTAGGGCCAAAATTTCAATA 59.105 34.615 6.18 0.00 0.00 1.90
2923 3498 2.105477 ACTGCATCCTTATACCCAGCTG 59.895 50.000 6.78 6.78 0.00 4.24
2929 3504 5.300752 CATCCTTATACCCAGCTGTGTTAG 58.699 45.833 13.81 5.97 0.00 2.34
3060 3714 7.893302 TGGTTTACATATTGATCCTGAGGTTTT 59.107 33.333 0.00 0.00 0.00 2.43
3061 3715 8.190784 GGTTTACATATTGATCCTGAGGTTTTG 58.809 37.037 0.00 0.00 0.00 2.44
3160 3815 4.386652 GGCATTTTGTTGCTACTGTGAATG 59.613 41.667 0.00 6.13 42.38 2.67
3223 3880 3.920454 TGTGCTACACTCAGGGACACTG 61.920 54.545 0.00 0.00 39.26 3.66
3234 3891 0.396811 GGGACACTGGCTACACTTGT 59.603 55.000 0.00 0.00 0.00 3.16
3333 3993 5.647225 ACAATGCTGGTCAATTTGTTTTGTT 59.353 32.000 0.00 0.00 26.69 2.83
3334 3995 5.738118 ATGCTGGTCAATTTGTTTTGTTG 57.262 34.783 0.00 0.00 0.00 3.33
3346 4007 5.597813 TTGTTTTGTTGAAATGTTGCGTT 57.402 30.435 0.00 0.00 0.00 4.84
3506 4170 5.163550 GGCAAACCTTGTTACTCTTGTCTTT 60.164 40.000 0.00 0.00 0.00 2.52
3520 4184 8.608844 ACTCTTGTCTTTTCAAAGATATCGTT 57.391 30.769 5.30 0.00 45.83 3.85
3969 4679 0.324943 TGGAGGAAGAAAGCGAAGGG 59.675 55.000 0.00 0.00 0.00 3.95
4014 4724 2.017782 CAGATCGAGAAGAACCGAGGA 58.982 52.381 0.00 0.00 38.25 3.71
4017 4727 2.775911 TCGAGAAGAACCGAGGACTA 57.224 50.000 0.00 0.00 0.00 2.59
4020 4730 2.748532 CGAGAAGAACCGAGGACTAACT 59.251 50.000 0.00 0.00 0.00 2.24
4050 4760 6.138761 CAGAAACAAGAAACTCAAGAATCCG 58.861 40.000 0.00 0.00 0.00 4.18
4228 4938 3.302480 GCCTTATCGTGAATGTACGCAAG 60.302 47.826 0.00 0.00 43.40 4.01
4292 5002 5.255710 TCGTTTGATGGTCATTTGTGTTT 57.744 34.783 0.00 0.00 0.00 2.83
4401 5112 3.726557 TCTGCCTTCAGATGTTGGATT 57.273 42.857 0.00 0.00 43.95 3.01
4411 5122 6.258230 TCAGATGTTGGATTGTGTTTGATC 57.742 37.500 0.00 0.00 0.00 2.92
4459 5170 3.515901 ACTACCAGTTCCCATCTCACTTC 59.484 47.826 0.00 0.00 0.00 3.01
4463 5174 4.407296 ACCAGTTCCCATCTCACTTCTATC 59.593 45.833 0.00 0.00 0.00 2.08
4510 5221 1.942657 GCTGTGCTCAAAACAGTCAGA 59.057 47.619 5.55 0.00 45.58 3.27
4512 5223 3.181497 GCTGTGCTCAAAACAGTCAGAAA 60.181 43.478 5.55 0.00 45.58 2.52
4607 5327 0.250234 TCGCTGGACTGGAATCCTTG 59.750 55.000 0.00 0.00 39.75 3.61
4608 5328 0.036010 CGCTGGACTGGAATCCTTGT 60.036 55.000 0.00 0.00 39.75 3.16
4738 5873 3.248602 GTCCATTCATGTATTCGCTGGAC 59.751 47.826 6.37 6.37 42.93 4.02
4755 5890 9.656040 TTCGCTGGACTAGTAAATTTTGTAATA 57.344 29.630 0.00 0.00 0.00 0.98
4756 5891 9.826574 TCGCTGGACTAGTAAATTTTGTAATAT 57.173 29.630 0.00 0.00 0.00 1.28
4813 5948 6.154706 AGAGGACCTCGAACTACATAATGTTT 59.845 38.462 15.97 0.00 35.36 2.83
4823 5958 7.281324 CGAACTACATAATGTTTATTGTGGGGA 59.719 37.037 0.00 0.00 39.06 4.81
4874 6009 9.900112 ATAAGTAGGAGAACAATTATACTCCCT 57.100 33.333 15.62 7.92 46.88 4.20
4875 6010 7.842887 AGTAGGAGAACAATTATACTCCCTC 57.157 40.000 15.62 11.14 46.88 4.30
4876 6011 7.597327 AGTAGGAGAACAATTATACTCCCTCT 58.403 38.462 15.62 12.51 46.88 3.69
4877 6012 6.739331 AGGAGAACAATTATACTCCCTCTG 57.261 41.667 15.62 0.00 46.88 3.35
4878 6013 6.206042 AGGAGAACAATTATACTCCCTCTGT 58.794 40.000 15.62 1.06 46.88 3.41
4879 6014 6.674419 AGGAGAACAATTATACTCCCTCTGTT 59.326 38.462 15.62 0.00 46.88 3.16
4880 6015 6.987404 GGAGAACAATTATACTCCCTCTGTTC 59.013 42.308 0.00 4.31 41.89 3.18
4881 6016 6.890293 AGAACAATTATACTCCCTCTGTTCC 58.110 40.000 8.08 0.00 41.19 3.62
4882 6017 5.632034 ACAATTATACTCCCTCTGTTCCC 57.368 43.478 0.00 0.00 0.00 3.97
4883 6018 5.036916 ACAATTATACTCCCTCTGTTCCCA 58.963 41.667 0.00 0.00 0.00 4.37
4884 6019 5.491078 ACAATTATACTCCCTCTGTTCCCAA 59.509 40.000 0.00 0.00 0.00 4.12
4885 6020 6.011981 ACAATTATACTCCCTCTGTTCCCAAA 60.012 38.462 0.00 0.00 0.00 3.28
4886 6021 6.848562 ATTATACTCCCTCTGTTCCCAAAT 57.151 37.500 0.00 0.00 0.00 2.32
4887 6022 7.947782 ATTATACTCCCTCTGTTCCCAAATA 57.052 36.000 0.00 0.00 0.00 1.40
4888 6023 5.632034 ATACTCCCTCTGTTCCCAAATAC 57.368 43.478 0.00 0.00 0.00 1.89
4889 6024 3.256704 ACTCCCTCTGTTCCCAAATACA 58.743 45.455 0.00 0.00 0.00 2.29
4890 6025 3.655777 ACTCCCTCTGTTCCCAAATACAA 59.344 43.478 0.00 0.00 0.00 2.41
4891 6026 4.263506 ACTCCCTCTGTTCCCAAATACAAG 60.264 45.833 0.00 0.00 0.00 3.16
4892 6027 3.655777 TCCCTCTGTTCCCAAATACAAGT 59.344 43.478 0.00 0.00 0.00 3.16
4893 6028 4.010349 CCCTCTGTTCCCAAATACAAGTC 58.990 47.826 0.00 0.00 0.00 3.01
4894 6029 4.263506 CCCTCTGTTCCCAAATACAAGTCT 60.264 45.833 0.00 0.00 0.00 3.24
4895 6030 5.316987 CCTCTGTTCCCAAATACAAGTCTT 58.683 41.667 0.00 0.00 0.00 3.01
4896 6031 5.770162 CCTCTGTTCCCAAATACAAGTCTTT 59.230 40.000 0.00 0.00 0.00 2.52
4897 6032 6.072452 CCTCTGTTCCCAAATACAAGTCTTTC 60.072 42.308 0.00 0.00 0.00 2.62
4898 6033 6.601332 TCTGTTCCCAAATACAAGTCTTTCT 58.399 36.000 0.00 0.00 0.00 2.52
4899 6034 7.741785 TCTGTTCCCAAATACAAGTCTTTCTA 58.258 34.615 0.00 0.00 0.00 2.10
4900 6035 7.878127 TCTGTTCCCAAATACAAGTCTTTCTAG 59.122 37.037 0.00 0.00 0.00 2.43
4901 6036 7.741785 TGTTCCCAAATACAAGTCTTTCTAGA 58.258 34.615 0.00 0.00 0.00 2.43
4902 6037 8.215050 TGTTCCCAAATACAAGTCTTTCTAGAA 58.785 33.333 0.00 0.00 30.65 2.10
4903 6038 9.063615 GTTCCCAAATACAAGTCTTTCTAGAAA 57.936 33.333 16.85 16.85 30.65 2.52
4904 6039 9.807921 TTCCCAAATACAAGTCTTTCTAGAAAT 57.192 29.630 18.02 5.28 30.65 2.17
4905 6040 9.807921 TCCCAAATACAAGTCTTTCTAGAAATT 57.192 29.630 18.02 7.47 30.65 1.82
4911 6046 9.793259 ATACAAGTCTTTCTAGAAATTCCAACA 57.207 29.630 18.02 3.49 30.65 3.33
4912 6047 8.519799 ACAAGTCTTTCTAGAAATTCCAACAA 57.480 30.769 18.02 0.00 30.65 2.83
4913 6048 8.966868 ACAAGTCTTTCTAGAAATTCCAACAAA 58.033 29.630 18.02 0.00 30.65 2.83
4914 6049 9.971922 CAAGTCTTTCTAGAAATTCCAACAAAT 57.028 29.630 18.02 1.93 30.65 2.32
4915 6050 9.971922 AAGTCTTTCTAGAAATTCCAACAAATG 57.028 29.630 18.02 2.79 30.65 2.32
4916 6051 9.354673 AGTCTTTCTAGAAATTCCAACAAATGA 57.645 29.630 18.02 5.04 30.65 2.57
4917 6052 9.399403 GTCTTTCTAGAAATTCCAACAAATGAC 57.601 33.333 18.02 12.64 30.65 3.06
4918 6053 9.354673 TCTTTCTAGAAATTCCAACAAATGACT 57.645 29.630 18.02 0.00 0.00 3.41
4921 6056 9.567776 TTCTAGAAATTCCAACAAATGACTACA 57.432 29.630 1.68 0.00 0.00 2.74
4922 6057 9.739276 TCTAGAAATTCCAACAAATGACTACAT 57.261 29.630 0.00 0.00 38.50 2.29
4925 6060 9.520515 AGAAATTCCAACAAATGACTACATACT 57.479 29.630 0.00 0.00 35.50 2.12
4926 6061 9.559958 GAAATTCCAACAAATGACTACATACTG 57.440 33.333 0.00 0.00 35.50 2.74
4927 6062 8.862325 AATTCCAACAAATGACTACATACTGA 57.138 30.769 0.00 0.00 35.50 3.41
4928 6063 7.905604 TTCCAACAAATGACTACATACTGAG 57.094 36.000 0.00 0.00 35.50 3.35
4929 6064 5.874810 TCCAACAAATGACTACATACTGAGC 59.125 40.000 0.00 0.00 35.50 4.26
4930 6065 5.643348 CCAACAAATGACTACATACTGAGCA 59.357 40.000 0.00 0.00 35.50 4.26
4931 6066 6.149308 CCAACAAATGACTACATACTGAGCAA 59.851 38.462 0.00 0.00 35.50 3.91
4932 6067 7.308529 CCAACAAATGACTACATACTGAGCAAA 60.309 37.037 0.00 0.00 35.50 3.68
4933 6068 7.744087 ACAAATGACTACATACTGAGCAAAA 57.256 32.000 0.00 0.00 35.50 2.44
4934 6069 8.340618 ACAAATGACTACATACTGAGCAAAAT 57.659 30.769 0.00 0.00 35.50 1.82
4935 6070 8.239314 ACAAATGACTACATACTGAGCAAAATG 58.761 33.333 0.00 0.00 35.50 2.32
4936 6071 8.453320 CAAATGACTACATACTGAGCAAAATGA 58.547 33.333 0.00 0.00 35.50 2.57
4937 6072 7.783090 ATGACTACATACTGAGCAAAATGAG 57.217 36.000 0.00 0.00 34.71 2.90
4938 6073 6.701340 TGACTACATACTGAGCAAAATGAGT 58.299 36.000 0.00 0.00 0.00 3.41
4939 6074 6.591448 TGACTACATACTGAGCAAAATGAGTG 59.409 38.462 0.00 0.00 0.00 3.51
4940 6075 6.701340 ACTACATACTGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
4941 6076 7.161404 ACTACATACTGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
4942 6077 7.826252 ACTACATACTGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
4943 6078 7.081526 ACATACTGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.00 0.00 2.52
4944 6079 6.883217 ACATACTGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.00 0.00 2.40
4945 6080 8.043113 ACATACTGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.00 0.00 1.98
4946 6081 6.734104 ACTGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
4947 6082 6.233434 ACTGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.00 0.00 2.74
4948 6083 6.148480 ACTGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
4985 6120 8.965986 TCTATATACATTCGTATGTTGCAGTC 57.034 34.615 13.12 0.00 42.29 3.51
4986 6121 8.027189 TCTATATACATTCGTATGTTGCAGTCC 58.973 37.037 13.12 0.00 42.29 3.85
4987 6122 3.052455 ACATTCGTATGTTGCAGTCCA 57.948 42.857 1.31 0.00 42.29 4.02
4988 6123 3.609853 ACATTCGTATGTTGCAGTCCAT 58.390 40.909 1.31 0.00 42.29 3.41
4989 6124 4.009675 ACATTCGTATGTTGCAGTCCATT 58.990 39.130 1.31 0.00 42.29 3.16
4990 6125 4.458989 ACATTCGTATGTTGCAGTCCATTT 59.541 37.500 1.31 0.00 42.29 2.32
4991 6126 5.645929 ACATTCGTATGTTGCAGTCCATTTA 59.354 36.000 1.31 0.00 42.29 1.40
4992 6127 6.150307 ACATTCGTATGTTGCAGTCCATTTAA 59.850 34.615 1.31 0.00 42.29 1.52
4993 6128 6.561737 TTCGTATGTTGCAGTCCATTTAAA 57.438 33.333 0.00 0.00 0.00 1.52
4994 6129 6.561737 TCGTATGTTGCAGTCCATTTAAAA 57.438 33.333 0.00 0.00 0.00 1.52
4995 6130 7.151999 TCGTATGTTGCAGTCCATTTAAAAT 57.848 32.000 0.00 0.00 0.00 1.82
4996 6131 7.026562 TCGTATGTTGCAGTCCATTTAAAATG 58.973 34.615 0.00 0.00 0.00 2.32
4997 6132 6.806249 CGTATGTTGCAGTCCATTTAAAATGT 59.194 34.615 0.00 0.00 0.00 2.71
4998 6133 7.008266 CGTATGTTGCAGTCCATTTAAAATGTC 59.992 37.037 0.00 0.00 0.00 3.06
4999 6134 6.403866 TGTTGCAGTCCATTTAAAATGTCT 57.596 33.333 0.00 0.00 0.00 3.41
5000 6135 7.517614 TGTTGCAGTCCATTTAAAATGTCTA 57.482 32.000 0.00 0.00 0.00 2.59
5001 6136 7.946207 TGTTGCAGTCCATTTAAAATGTCTAA 58.054 30.769 0.00 0.00 0.00 2.10
5002 6137 8.417106 TGTTGCAGTCCATTTAAAATGTCTAAA 58.583 29.630 0.00 0.00 0.00 1.85
5003 6138 9.255304 GTTGCAGTCCATTTAAAATGTCTAAAA 57.745 29.630 0.00 0.00 0.00 1.52
5004 6139 9.823647 TTGCAGTCCATTTAAAATGTCTAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
5005 6140 9.474920 TGCAGTCCATTTAAAATGTCTAAAAAG 57.525 29.630 0.00 0.00 0.00 2.27
5006 6141 9.691362 GCAGTCCATTTAAAATGTCTAAAAAGA 57.309 29.630 0.00 0.00 0.00 2.52
5026 6161 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
5027 6162 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
5028 6163 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
5029 6164 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
5030 6165 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
5031 6166 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
5044 6179 4.276678 CGGAGGGAGTATATGTCAACGTAA 59.723 45.833 0.00 0.00 0.00 3.18
5045 6180 5.527033 GGAGGGAGTATATGTCAACGTAAC 58.473 45.833 0.00 0.00 0.00 2.50
5049 6184 6.039493 AGGGAGTATATGTCAACGTAACAGAG 59.961 42.308 9.27 0.00 0.00 3.35
5109 6247 2.100252 GGAGGCATGGACATTGTCATTG 59.900 50.000 18.09 14.49 33.68 2.82
5128 6266 7.280876 TGTCATTGTAGTCTGCTGGAATATTTC 59.719 37.037 0.00 0.00 0.00 2.17
5232 6371 3.070159 TCTCCTTGGTCACAGAGTCAAAG 59.930 47.826 0.00 0.00 0.00 2.77
5259 6399 2.009681 TGCAGACACCTTGGAGAGTA 57.990 50.000 0.00 0.00 0.00 2.59
5265 6405 4.223923 CAGACACCTTGGAGAGTAGGATTT 59.776 45.833 0.00 0.00 35.45 2.17
5283 6423 6.071984 AGGATTTACACTCGTCTAGGATGAT 58.928 40.000 0.00 0.00 0.00 2.45
5284 6424 6.551601 AGGATTTACACTCGTCTAGGATGATT 59.448 38.462 0.00 0.00 0.00 2.57
5330 6470 4.013267 ACTCTGAACCTCATGTTTCCTG 57.987 45.455 0.00 0.00 37.29 3.86
5331 6471 3.392616 ACTCTGAACCTCATGTTTCCTGT 59.607 43.478 0.00 0.00 37.29 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.958822 ATTCTTTTGTGCGTCACCCC 59.041 50.000 7.38 0.00 32.73 4.95
28 29 7.379529 AGTGAAAGACAATTATTCTTTTGTGCG 59.620 33.333 13.02 0.00 42.21 5.34
61 62 5.362430 AGGTTTTGTGCTTCTGTATTTTCCA 59.638 36.000 0.00 0.00 0.00 3.53
62 63 5.842907 AGGTTTTGTGCTTCTGTATTTTCC 58.157 37.500 0.00 0.00 0.00 3.13
230 256 3.060978 ACTTTCGCGGTTTTCTGTTTC 57.939 42.857 6.13 0.00 0.00 2.78
487 600 6.312672 ACCGGAAAACAGAAACAAAAATCAAG 59.687 34.615 9.46 0.00 0.00 3.02
488 601 6.166982 ACCGGAAAACAGAAACAAAAATCAA 58.833 32.000 9.46 0.00 0.00 2.57
490 603 6.533723 AGAACCGGAAAACAGAAACAAAAATC 59.466 34.615 9.46 0.00 0.00 2.17
491 604 6.403049 AGAACCGGAAAACAGAAACAAAAAT 58.597 32.000 9.46 0.00 0.00 1.82
578 691 3.451141 TTCACCATTGTGTTTCTTGCC 57.549 42.857 0.00 0.00 43.26 4.52
581 694 7.201513 CGAACAATTTTCACCATTGTGTTTCTT 60.202 33.333 0.00 0.00 42.80 2.52
682 796 6.639279 GCTCGAGGTTTTGTGCTTTTATTTTA 59.361 34.615 15.58 0.00 0.00 1.52
704 818 2.854185 GTGTGAAACTTGTTGCAAGCTC 59.146 45.455 0.00 6.68 38.04 4.09
833 1007 1.310904 TTCGGTTTTTGGTTAGCGCT 58.689 45.000 17.26 17.26 35.43 5.92
855 1029 2.973945 ACTCGGCCTAGAAATCAACAC 58.026 47.619 11.98 0.00 0.00 3.32
925 1099 0.671781 AGCAGCGAAATGAAGCGAGT 60.672 50.000 0.00 0.00 38.61 4.18
926 1100 0.026027 GAGCAGCGAAATGAAGCGAG 59.974 55.000 0.00 0.00 38.61 5.03
939 1113 4.219846 CTGTGCGATGCGAGCAGC 62.220 66.667 2.91 2.91 46.10 5.25
967 1141 2.709934 CTGTGGAAGGAGATGGATGGAT 59.290 50.000 0.00 0.00 0.00 3.41
1315 1495 2.119655 GTCCTCGCCTCCTTCGCTA 61.120 63.158 0.00 0.00 0.00 4.26
1396 1576 6.813649 CAGTATATGATTTGTCCCATACCTCG 59.186 42.308 0.00 0.00 0.00 4.63
1588 1768 0.252239 TCTCTGCCTGCAACCTCCTA 60.252 55.000 0.00 0.00 0.00 2.94
1671 1851 3.119096 GGTCGGACGCCTTTGAGC 61.119 66.667 1.43 0.00 0.00 4.26
2170 2350 7.550551 TCCAGAGCTAGTAAATTGTGAGATTTG 59.449 37.037 0.00 0.00 31.96 2.32
2178 2358 5.013183 ACCTTGTCCAGAGCTAGTAAATTGT 59.987 40.000 0.00 0.00 0.00 2.71
2527 2718 7.665690 ACCAACAACAATAAGAAACATGCATA 58.334 30.769 0.00 0.00 0.00 3.14
2533 2724 7.536855 ACGTAAACCAACAACAATAAGAAACA 58.463 30.769 0.00 0.00 0.00 2.83
2557 2748 8.064814 GCACAAGTTAAAATAGCTAGCTATGAC 58.935 37.037 32.67 25.96 39.03 3.06
2699 2901 5.404466 TTGAAATTTTGGCCCTACATGAG 57.596 39.130 0.00 0.00 0.00 2.90
2893 3463 6.998673 GGGTATAAGGATGCAGTTTCACTTAT 59.001 38.462 0.00 4.14 35.83 1.73
2897 3472 4.523083 TGGGTATAAGGATGCAGTTTCAC 58.477 43.478 0.00 0.00 0.00 3.18
2923 3498 6.367422 GTGCTGGCTGATAATATCTCTAACAC 59.633 42.308 1.66 1.01 0.00 3.32
2929 3504 6.638610 AGTATGTGCTGGCTGATAATATCTC 58.361 40.000 1.66 0.00 0.00 2.75
2987 3639 8.893727 CCTAATAATCCTCGAATTTCACAAACT 58.106 33.333 0.00 0.00 0.00 2.66
3060 3714 4.957759 TTGAACTCGAGACATATCGACA 57.042 40.909 21.68 2.75 46.20 4.35
3061 3715 6.073167 TCCTATTGAACTCGAGACATATCGAC 60.073 42.308 21.68 0.21 46.20 4.20
3223 3880 1.002544 AGCTGGAAGACAAGTGTAGCC 59.997 52.381 0.00 0.00 34.07 3.93
3234 3891 4.278419 GCCAGAGTTTTTAAAGCTGGAAGA 59.722 41.667 22.19 0.00 41.01 2.87
3333 3993 4.495911 TCAAGCATAACGCAACATTTCA 57.504 36.364 0.00 0.00 46.13 2.69
3334 3995 5.801947 AGATTCAAGCATAACGCAACATTTC 59.198 36.000 0.00 0.00 46.13 2.17
3346 4007 4.219070 ACAAAGCAGCAAGATTCAAGCATA 59.781 37.500 0.00 0.00 0.00 3.14
3393 4054 0.535102 AAGGCTGTTCTGGAACACCG 60.535 55.000 11.53 5.45 45.42 4.94
3395 4056 2.024414 ACAAAGGCTGTTCTGGAACAC 58.976 47.619 11.53 8.98 45.42 3.32
3506 4170 9.361315 TCGAGTATTTCAAACGATATCTTTGAA 57.639 29.630 24.11 24.11 42.94 2.69
3969 4679 2.615912 CGAAATCTTCCTCTTGCCATCC 59.384 50.000 0.00 0.00 0.00 3.51
4014 4724 3.321111 TCTTGTTTCTGGAGCGAGTTAGT 59.679 43.478 0.00 0.00 0.00 2.24
4017 4727 2.910688 TCTTGTTTCTGGAGCGAGTT 57.089 45.000 0.00 0.00 0.00 3.01
4020 4730 3.131396 GAGTTTCTTGTTTCTGGAGCGA 58.869 45.455 0.00 0.00 0.00 4.93
4050 4760 6.018669 CACTCTTAATCCTGTATTTCTTCCGC 60.019 42.308 0.00 0.00 0.00 5.54
4079 4789 3.908103 ACCTTGCCTCCTTTTACTCTGTA 59.092 43.478 0.00 0.00 0.00 2.74
4167 4877 1.624336 ACCTAACACTACGGCTGACA 58.376 50.000 0.00 0.00 0.00 3.58
4228 4938 6.074729 GCGAACTAAACCATACCAAACAAAAC 60.075 38.462 0.00 0.00 0.00 2.43
4240 4950 0.675522 CCCCACGCGAACTAAACCAT 60.676 55.000 15.93 0.00 0.00 3.55
4292 5002 6.887013 TCCACCAAAACTGTTTACTACTACA 58.113 36.000 6.16 0.00 0.00 2.74
4401 5112 5.000591 TGCTTCTAATTCCGATCAAACACA 58.999 37.500 0.00 0.00 0.00 3.72
4411 5122 6.536582 TCTTCATCTTTCTGCTTCTAATTCCG 59.463 38.462 0.00 0.00 0.00 4.30
4449 5160 5.527951 AGCATTTGCAGATAGAAGTGAGATG 59.472 40.000 5.20 0.00 45.16 2.90
4463 5174 9.740239 AACATTATGTAATAGAAGCATTTGCAG 57.260 29.630 5.20 0.00 45.16 4.41
4534 5250 7.935210 GGATCCAAATGCTCCAAAAATCATATT 59.065 33.333 6.95 0.00 0.00 1.28
4701 5836 4.929211 TGAATGGACGAGTGTTTGATAGTG 59.071 41.667 0.00 0.00 0.00 2.74
4780 5915 3.578716 AGTTCGAGGTCCTCTTTGATTCA 59.421 43.478 17.00 0.00 0.00 2.57
4813 5948 5.192722 TGATGTAATCCTTGTCCCCACAATA 59.807 40.000 0.00 0.00 44.73 1.90
4861 5996 5.630415 TGGGAACAGAGGGAGTATAATTG 57.370 43.478 0.00 0.00 35.01 2.32
4869 6004 4.263506 ACTTGTATTTGGGAACAGAGGGAG 60.264 45.833 0.00 0.00 44.54 4.30
4870 6005 3.655777 ACTTGTATTTGGGAACAGAGGGA 59.344 43.478 0.00 0.00 44.54 4.20
4871 6006 4.010349 GACTTGTATTTGGGAACAGAGGG 58.990 47.826 0.00 0.00 44.54 4.30
4872 6007 4.911390 AGACTTGTATTTGGGAACAGAGG 58.089 43.478 0.00 0.00 44.54 3.69
4873 6008 6.712547 AGAAAGACTTGTATTTGGGAACAGAG 59.287 38.462 0.00 0.00 44.54 3.35
4874 6009 6.601332 AGAAAGACTTGTATTTGGGAACAGA 58.399 36.000 0.00 0.00 44.54 3.41
4875 6010 6.884280 AGAAAGACTTGTATTTGGGAACAG 57.116 37.500 0.00 0.00 44.54 3.16
4876 6011 7.741785 TCTAGAAAGACTTGTATTTGGGAACA 58.258 34.615 0.00 0.00 39.83 3.18
4877 6012 8.617290 TTCTAGAAAGACTTGTATTTGGGAAC 57.383 34.615 1.68 0.00 0.00 3.62
4878 6013 9.807921 ATTTCTAGAAAGACTTGTATTTGGGAA 57.192 29.630 21.75 0.00 33.32 3.97
4879 6014 9.807921 AATTTCTAGAAAGACTTGTATTTGGGA 57.192 29.630 21.75 0.00 33.32 4.37
4885 6020 9.793259 TGTTGGAATTTCTAGAAAGACTTGTAT 57.207 29.630 21.75 1.29 33.32 2.29
4886 6021 9.621629 TTGTTGGAATTTCTAGAAAGACTTGTA 57.378 29.630 21.75 5.44 33.32 2.41
4887 6022 8.519799 TTGTTGGAATTTCTAGAAAGACTTGT 57.480 30.769 21.75 2.71 33.32 3.16
4888 6023 9.971922 ATTTGTTGGAATTTCTAGAAAGACTTG 57.028 29.630 21.75 0.00 33.32 3.16
4889 6024 9.971922 CATTTGTTGGAATTTCTAGAAAGACTT 57.028 29.630 21.75 12.28 33.32 3.01
4890 6025 9.354673 TCATTTGTTGGAATTTCTAGAAAGACT 57.645 29.630 21.75 9.93 33.32 3.24
4891 6026 9.399403 GTCATTTGTTGGAATTTCTAGAAAGAC 57.601 33.333 21.75 16.79 33.32 3.01
4892 6027 9.354673 AGTCATTTGTTGGAATTTCTAGAAAGA 57.645 29.630 21.75 7.50 33.32 2.52
4895 6030 9.567776 TGTAGTCATTTGTTGGAATTTCTAGAA 57.432 29.630 0.00 0.00 0.00 2.10
4896 6031 9.739276 ATGTAGTCATTTGTTGGAATTTCTAGA 57.261 29.630 0.00 0.00 0.00 2.43
4899 6034 9.520515 AGTATGTAGTCATTTGTTGGAATTTCT 57.479 29.630 0.00 0.00 35.70 2.52
4900 6035 9.559958 CAGTATGTAGTCATTTGTTGGAATTTC 57.440 33.333 0.00 0.00 35.70 2.17
4901 6036 9.295825 TCAGTATGTAGTCATTTGTTGGAATTT 57.704 29.630 0.00 0.00 37.40 1.82
4902 6037 8.862325 TCAGTATGTAGTCATTTGTTGGAATT 57.138 30.769 0.00 0.00 37.40 2.17
4903 6038 7.066284 GCTCAGTATGTAGTCATTTGTTGGAAT 59.934 37.037 0.00 0.00 37.40 3.01
4904 6039 6.371548 GCTCAGTATGTAGTCATTTGTTGGAA 59.628 38.462 0.00 0.00 37.40 3.53
4905 6040 5.874810 GCTCAGTATGTAGTCATTTGTTGGA 59.125 40.000 0.00 0.00 37.40 3.53
4906 6041 5.643348 TGCTCAGTATGTAGTCATTTGTTGG 59.357 40.000 0.00 0.00 37.40 3.77
4907 6042 6.726258 TGCTCAGTATGTAGTCATTTGTTG 57.274 37.500 0.00 0.00 37.40 3.33
4908 6043 7.744087 TTTGCTCAGTATGTAGTCATTTGTT 57.256 32.000 0.00 0.00 37.40 2.83
4909 6044 7.744087 TTTTGCTCAGTATGTAGTCATTTGT 57.256 32.000 0.00 0.00 37.40 2.83
4910 6045 8.453320 TCATTTTGCTCAGTATGTAGTCATTTG 58.547 33.333 0.00 0.00 37.40 2.32
4911 6046 8.565896 TCATTTTGCTCAGTATGTAGTCATTT 57.434 30.769 0.00 0.00 37.40 2.32
4912 6047 7.826252 ACTCATTTTGCTCAGTATGTAGTCATT 59.174 33.333 0.00 0.00 37.40 2.57
4913 6048 7.279536 CACTCATTTTGCTCAGTATGTAGTCAT 59.720 37.037 0.00 0.00 37.40 3.06
4914 6049 6.591448 CACTCATTTTGCTCAGTATGTAGTCA 59.409 38.462 0.00 0.00 37.40 3.41
4915 6050 6.813649 TCACTCATTTTGCTCAGTATGTAGTC 59.186 38.462 0.00 0.00 37.40 2.59
4916 6051 6.701340 TCACTCATTTTGCTCAGTATGTAGT 58.299 36.000 0.00 0.00 37.40 2.73
4917 6052 7.601073 TTCACTCATTTTGCTCAGTATGTAG 57.399 36.000 0.00 0.00 37.40 2.74
4918 6053 8.043113 AGATTCACTCATTTTGCTCAGTATGTA 58.957 33.333 0.00 0.00 37.40 2.29
4919 6054 6.883217 AGATTCACTCATTTTGCTCAGTATGT 59.117 34.615 0.00 0.00 37.40 2.29
4920 6055 7.317842 AGATTCACTCATTTTGCTCAGTATG 57.682 36.000 0.00 0.00 37.54 2.39
4921 6056 8.043113 TGTAGATTCACTCATTTTGCTCAGTAT 58.957 33.333 0.00 0.00 0.00 2.12
4922 6057 7.331934 GTGTAGATTCACTCATTTTGCTCAGTA 59.668 37.037 0.00 0.00 35.68 2.74
4923 6058 6.148480 GTGTAGATTCACTCATTTTGCTCAGT 59.852 38.462 0.00 0.00 35.68 3.41
4924 6059 6.370994 AGTGTAGATTCACTCATTTTGCTCAG 59.629 38.462 0.00 0.00 44.07 3.35
4925 6060 6.233434 AGTGTAGATTCACTCATTTTGCTCA 58.767 36.000 0.00 0.00 44.07 4.26
4926 6061 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4959 6094 9.574458 GACTGCAACATACGAATGTATATAGAT 57.426 33.333 0.00 0.00 45.79 1.98
4960 6095 8.027189 GGACTGCAACATACGAATGTATATAGA 58.973 37.037 0.00 0.00 45.79 1.98
4961 6096 7.812669 TGGACTGCAACATACGAATGTATATAG 59.187 37.037 0.00 0.00 45.79 1.31
4962 6097 7.662897 TGGACTGCAACATACGAATGTATATA 58.337 34.615 0.00 0.00 45.79 0.86
4963 6098 6.521162 TGGACTGCAACATACGAATGTATAT 58.479 36.000 0.00 0.00 45.79 0.86
4964 6099 5.908341 TGGACTGCAACATACGAATGTATA 58.092 37.500 0.00 0.00 45.79 1.47
4965 6100 4.765273 TGGACTGCAACATACGAATGTAT 58.235 39.130 0.00 0.00 45.79 2.29
4966 6101 4.195225 TGGACTGCAACATACGAATGTA 57.805 40.909 0.00 0.00 45.79 2.29
4968 6103 4.621068 AATGGACTGCAACATACGAATG 57.379 40.909 0.00 0.00 39.17 2.67
4969 6104 6.751514 TTAAATGGACTGCAACATACGAAT 57.248 33.333 0.00 0.00 0.00 3.34
4970 6105 6.561737 TTTAAATGGACTGCAACATACGAA 57.438 33.333 0.00 0.00 0.00 3.85
4971 6106 6.561737 TTTTAAATGGACTGCAACATACGA 57.438 33.333 0.00 0.00 0.00 3.43
4972 6107 6.806249 ACATTTTAAATGGACTGCAACATACG 59.194 34.615 20.00 0.00 0.00 3.06
4973 6108 8.028938 AGACATTTTAAATGGACTGCAACATAC 58.971 33.333 20.00 0.00 0.00 2.39
4974 6109 8.121305 AGACATTTTAAATGGACTGCAACATA 57.879 30.769 20.00 0.00 0.00 2.29
4975 6110 6.996509 AGACATTTTAAATGGACTGCAACAT 58.003 32.000 20.00 0.00 0.00 2.71
4976 6111 6.403866 AGACATTTTAAATGGACTGCAACA 57.596 33.333 20.00 0.00 0.00 3.33
4977 6112 8.810652 TTTAGACATTTTAAATGGACTGCAAC 57.189 30.769 20.00 3.56 0.00 4.17
4978 6113 9.823647 TTTTTAGACATTTTAAATGGACTGCAA 57.176 25.926 20.00 12.79 0.00 4.08
4979 6114 9.474920 CTTTTTAGACATTTTAAATGGACTGCA 57.525 29.630 20.00 8.76 0.00 4.41
4980 6115 9.691362 TCTTTTTAGACATTTTAAATGGACTGC 57.309 29.630 20.00 5.86 0.00 4.40
5000 6135 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
5001 6136 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
5002 6137 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
5003 6138 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
5004 6139 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
5005 6140 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
5006 6141 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
5007 6142 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
5009 6144 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
5010 6145 7.899709 ACATATACTCCCTCCGTTCCTAAATAT 59.100 37.037 0.00 0.00 0.00 1.28
5011 6146 7.243824 ACATATACTCCCTCCGTTCCTAAATA 58.756 38.462 0.00 0.00 0.00 1.40
5012 6147 6.082707 ACATATACTCCCTCCGTTCCTAAAT 58.917 40.000 0.00 0.00 0.00 1.40
5013 6148 5.461327 ACATATACTCCCTCCGTTCCTAAA 58.539 41.667 0.00 0.00 0.00 1.85
5014 6149 5.070823 ACATATACTCCCTCCGTTCCTAA 57.929 43.478 0.00 0.00 0.00 2.69
5015 6150 4.105217 TGACATATACTCCCTCCGTTCCTA 59.895 45.833 0.00 0.00 0.00 2.94
5016 6151 3.117246 TGACATATACTCCCTCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
5017 6152 3.228453 TGACATATACTCCCTCCGTTCC 58.772 50.000 0.00 0.00 0.00 3.62
5018 6153 4.618965 GTTGACATATACTCCCTCCGTTC 58.381 47.826 0.00 0.00 0.00 3.95
5019 6154 3.067742 CGTTGACATATACTCCCTCCGTT 59.932 47.826 0.00 0.00 0.00 4.44
5020 6155 2.621998 CGTTGACATATACTCCCTCCGT 59.378 50.000 0.00 0.00 0.00 4.69
5021 6156 2.621998 ACGTTGACATATACTCCCTCCG 59.378 50.000 0.00 0.00 0.00 4.63
5022 6157 5.068198 TGTTACGTTGACATATACTCCCTCC 59.932 44.000 0.00 0.00 0.00 4.30
5023 6158 6.039047 TCTGTTACGTTGACATATACTCCCTC 59.961 42.308 0.00 0.00 0.00 4.30
5024 6159 5.889853 TCTGTTACGTTGACATATACTCCCT 59.110 40.000 0.00 0.00 0.00 4.20
5025 6160 6.039047 TCTCTGTTACGTTGACATATACTCCC 59.961 42.308 0.00 0.00 0.00 4.30
5026 6161 7.012138 TCTCTCTGTTACGTTGACATATACTCC 59.988 40.741 0.00 0.00 0.00 3.85
5027 6162 7.917597 TCTCTCTGTTACGTTGACATATACTC 58.082 38.462 0.00 0.00 0.00 2.59
5028 6163 7.860918 TCTCTCTGTTACGTTGACATATACT 57.139 36.000 0.00 0.00 0.00 2.12
5029 6164 8.906636 TTTCTCTCTGTTACGTTGACATATAC 57.093 34.615 0.00 0.00 0.00 1.47
5030 6165 9.350357 GTTTTCTCTCTGTTACGTTGACATATA 57.650 33.333 0.00 0.00 0.00 0.86
5031 6166 7.331193 GGTTTTCTCTCTGTTACGTTGACATAT 59.669 37.037 0.00 0.00 0.00 1.78
5044 6179 6.777782 AGATGATTTCAGGTTTTCTCTCTGT 58.222 36.000 0.00 0.00 0.00 3.41
5045 6180 7.684937 AAGATGATTTCAGGTTTTCTCTCTG 57.315 36.000 0.00 0.00 0.00 3.35
5049 6184 5.866092 GGCAAAGATGATTTCAGGTTTTCTC 59.134 40.000 0.00 0.00 0.00 2.87
5109 6247 6.701841 TGATTCGAAATATTCCAGCAGACTAC 59.298 38.462 0.00 0.00 0.00 2.73
5128 6266 5.824904 ATGTTTCCCATTTCTCTGATTCG 57.175 39.130 0.00 0.00 0.00 3.34
5157 6295 1.068748 GTTGACTGCAGGCACTTCATG 60.069 52.381 25.40 0.00 34.60 3.07
5232 6371 2.227388 CCAAGGTGTCTGCATTCTTGTC 59.773 50.000 0.00 0.00 37.20 3.18
5259 6399 5.446860 TCATCCTAGACGAGTGTAAATCCT 58.553 41.667 0.00 0.00 0.00 3.24
5265 6405 6.071560 ACACAAAATCATCCTAGACGAGTGTA 60.072 38.462 0.00 0.00 34.03 2.90
5283 6423 4.705337 AAGGCGAAACTACAACACAAAA 57.295 36.364 0.00 0.00 0.00 2.44
5284 6424 4.634883 TGTAAGGCGAAACTACAACACAAA 59.365 37.500 0.00 0.00 0.00 2.83
5330 6470 3.471680 GAGATCATGGAAGGCCTGTTAC 58.528 50.000 5.69 0.00 34.31 2.50
5331 6471 2.439507 GGAGATCATGGAAGGCCTGTTA 59.560 50.000 5.69 0.00 34.31 2.41


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

AutoCloner maintained by Alex Coulton.