Multiple sequence alignment - TraesCS1D01G312700

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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 TraesCS1D01G312700 chr1D 100.000 4348 0 0 356 4703 408511089 408515436 0.000000e+00 8030.0
1 TraesCS1D01G312700 chr1D 100.000 36 0 0 1 36 408510734 408510769 3.040000e-07 67.6
2 TraesCS1D01G312700 chr1B 94.389 4010 204 11 356 4358 549781404 549785399 0.000000e+00 6139.0
3 TraesCS1D01G312700 chr1B 94.118 85 4 1 4591 4674 133188852 133188936 1.370000e-25 128.0
4 TraesCS1D01G312700 chr1B 100.000 33 0 0 1 33 549781339 549781371 1.410000e-05 62.1
5 TraesCS1D01G312700 chr1A 93.862 3894 208 17 356 4242 504578271 504582140 0.000000e+00 5838.0
6 TraesCS1D01G312700 chr1A 85.251 339 39 5 4237 4566 504585577 504585913 5.830000e-89 339.0
7 TraesCS1D01G312700 chr1A 97.222 36 1 0 1 36 504578208 504578243 1.410000e-05 62.1
8 TraesCS1D01G312700 chr5D 82.016 367 60 6 3082 3445 478163955 478163592 1.640000e-79 307.0
9 TraesCS1D01G312700 chr4A 86.260 131 17 1 2251 2380 730105989 730105859 1.760000e-29 141.0
10 TraesCS1D01G312700 chr7B 96.429 84 3 0 4591 4674 374713675 374713592 6.350000e-29 139.0
11 TraesCS1D01G312700 chr3D 92.632 95 7 0 4591 4685 331672517 331672423 2.280000e-28 137.0
12 TraesCS1D01G312700 chr3D 94.118 85 5 0 4590 4674 331672425 331672509 3.820000e-26 130.0
13 TraesCS1D01G312700 chr4D 93.258 89 5 1 4594 4682 293383757 293383844 3.820000e-26 130.0
14 TraesCS1D01G312700 chr2A 90.816 98 7 2 4592 4689 618434141 618434236 3.820000e-26 130.0
15 TraesCS1D01G312700 chr6D 95.062 81 4 0 4594 4674 302193796 302193876 1.370000e-25 128.0
16 TraesCS1D01G312700 chr5A 92.391 92 4 3 4594 4682 309680262 309680171 1.370000e-25 128.0
17 TraesCS1D01G312700 chr2B 94.048 84 5 0 4591 4674 79295651 79295734 1.370000e-25 128.0


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 TraesCS1D01G312700 chr1D 408510734 408515436 4702 False 4048.80 8030 100.000000 1 4703 2 chr1D.!!$F1 4702
1 TraesCS1D01G312700 chr1B 549781339 549785399 4060 False 3100.55 6139 97.194500 1 4358 2 chr1B.!!$F2 4357
2 TraesCS1D01G312700 chr1A 504578208 504585913 7705 False 2079.70 5838 92.111667 1 4566 3 chr1A.!!$F1 4565

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
811 823 0.108520 CTGCATGCCATTTGTGTCCC 60.109 55.0 16.68 0.00 0.00 4.46 F
814 826 0.109179 CATGCCATTTGTGTCCCACG 60.109 55.0 0.00 0.00 37.14 4.94 F
1964 1979 0.548682 AGGTGGAGAAGTGGAGGCAT 60.549 55.0 0.00 0.00 0.00 4.40 F
2622 2637 0.322975 GTGTCATCTCTGGGCAGTGT 59.677 55.0 0.00 0.00 0.00 3.55 F
3447 3462 0.034186 ATCTCATTTCCTTGGCGCCA 60.034 50.0 29.03 29.03 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2255 0.107508 ATGACCATCTGGCTTGGACG 60.108 55.000 8.38 0.0 39.32 4.79 R
2375 2390 1.918293 CCTCCACACCCCAGCTGTA 60.918 63.158 13.81 0.0 0.00 2.74 R
3426 3441 0.305922 GCGCCAAGGAAATGAGATCG 59.694 55.000 0.00 0.0 0.00 3.69 R
3480 3495 0.323302 TTGCTACGTTGATGGCTGGA 59.677 50.000 0.00 0.0 0.00 3.86 R
4681 8151 0.392461 GCGATGGTGGTGCCTAAAGA 60.392 55.000 0.00 0.0 38.35 2.52 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
387 388 3.815809 CTGTAGTGAAGAAACCCCACAA 58.184 45.455 0.00 0.00 33.53 3.33
389 390 3.201266 TGTAGTGAAGAAACCCCACAACT 59.799 43.478 0.00 0.00 33.53 3.16
478 479 9.616634 GCTACATTCACACAAATGATATATTGG 57.383 33.333 3.78 0.00 38.64 3.16
541 552 4.215399 AGAAGAGTGCTCTAGATACATCGC 59.785 45.833 1.77 2.01 39.39 4.58
567 578 4.137543 GGACCATAGATTGTGCTAAAGGG 58.862 47.826 0.00 0.00 0.00 3.95
613 624 0.178955 TACGACTCCCCACCAAGTGA 60.179 55.000 0.00 0.00 35.23 3.41
669 680 1.825474 CACTGGTCGGTAATGAGGACT 59.175 52.381 0.00 0.00 0.00 3.85
682 693 1.412710 TGAGGACTCGTGCTTCAACTT 59.587 47.619 0.00 0.00 0.00 2.66
706 717 1.076332 CGGATCGTTTCACCACTTCC 58.924 55.000 0.00 0.00 0.00 3.46
728 739 4.440525 CCAGAATCCACATTGCATGTTACC 60.441 45.833 0.00 0.00 42.70 2.85
738 749 6.712095 CACATTGCATGTTACCCTATCACTAT 59.288 38.462 0.00 0.00 42.70 2.12
811 823 0.108520 CTGCATGCCATTTGTGTCCC 60.109 55.000 16.68 0.00 0.00 4.46
814 826 0.109179 CATGCCATTTGTGTCCCACG 60.109 55.000 0.00 0.00 37.14 4.94
866 878 1.444895 GCATTGCGCCTTCAGTTGG 60.445 57.895 4.18 0.00 32.94 3.77
924 936 2.764010 AGTGTGTGACCAGTGAGTACAA 59.236 45.455 0.00 0.00 0.00 2.41
993 1005 1.134220 TGGTGGTGTGTGAGGAGTTTC 60.134 52.381 0.00 0.00 0.00 2.78
1015 1028 0.887247 TTTGATGGCACCATGGAACG 59.113 50.000 21.47 7.51 36.70 3.95
1025 1038 2.035626 ATGGAACGGCTTGTGGGG 59.964 61.111 0.00 0.00 0.00 4.96
1107 1120 2.170817 GGAGAACCCCAACTGGTCTATC 59.829 54.545 0.00 0.00 37.76 2.08
1260 1273 4.521062 GCGAGGCTCACATCCGCT 62.521 66.667 15.95 0.00 42.24 5.52
1358 1371 0.976073 GAGGATGTGGAGGAACGGGA 60.976 60.000 0.00 0.00 0.00 5.14
1460 1473 2.509336 CGCCTACTCCAACGGCAG 60.509 66.667 0.00 0.00 43.95 4.85
1463 1476 2.291043 CCTACTCCAACGGCAGGGT 61.291 63.158 0.00 0.00 0.00 4.34
1527 1540 1.897398 GCTTTCGTGCCACCTACGTG 61.897 60.000 0.00 0.00 41.91 4.49
1666 1679 1.530771 CCCCTCTCTCCAGCATTGG 59.469 63.158 0.00 0.00 46.49 3.16
1747 1760 1.660333 GCAACGAGAAAGAGGTTTGCG 60.660 52.381 0.00 0.00 0.00 4.85
1748 1761 1.597663 CAACGAGAAAGAGGTTTGCGT 59.402 47.619 0.00 0.00 35.78 5.24
1787 1800 2.917713 TGCCCCCACAGTTTCAATAT 57.082 45.000 0.00 0.00 0.00 1.28
1853 1868 4.214383 CGGCAGTCGATTGCAGCG 62.214 66.667 30.47 22.36 45.86 5.18
1901 1916 2.618241 CAACTTTCTTGTGCAGGTGCTA 59.382 45.455 3.18 0.00 42.66 3.49
1925 1940 1.079819 CTCCGATGACGTGGCAACT 60.080 57.895 0.00 0.00 37.88 3.16
1943 1958 4.674623 GCAACTCAGGCATTGATCAAAGAG 60.675 45.833 13.09 15.48 34.68 2.85
1964 1979 0.548682 AGGTGGAGAAGTGGAGGCAT 60.549 55.000 0.00 0.00 0.00 4.40
2144 2159 1.824852 GTGCCCCATTTTAAGGTGGAG 59.175 52.381 9.18 0.00 37.72 3.86
2149 2164 3.763897 CCCCATTTTAAGGTGGAGTTCAG 59.236 47.826 9.18 0.00 37.72 3.02
2150 2165 4.407365 CCCATTTTAAGGTGGAGTTCAGT 58.593 43.478 9.18 0.00 37.72 3.41
2158 2173 4.078639 AGGTGGAGTTCAGTTCTTGAAG 57.921 45.455 0.00 0.00 46.09 3.02
2167 2182 7.389053 GGAGTTCAGTTCTTGAAGTATGTGAAT 59.611 37.037 0.00 0.00 46.88 2.57
2240 2255 1.135333 GACAACGAGGATCTGGGTCTC 59.865 57.143 0.00 0.00 0.00 3.36
2375 2390 4.285863 TCAACTTCTTTGGGTTCAATGGT 58.714 39.130 0.00 0.00 35.69 3.55
2402 2417 1.077429 GGTGTGGAGGATCAAGGCC 60.077 63.158 0.00 0.00 36.25 5.19
2498 2513 2.554462 GGGCTGGAAGTTTGTCTTTCTC 59.446 50.000 0.00 0.00 36.40 2.87
2622 2637 0.322975 GTGTCATCTCTGGGCAGTGT 59.677 55.000 0.00 0.00 0.00 3.55
2671 2686 3.684103 CTTACCGAAAGCAACAACACA 57.316 42.857 0.00 0.00 0.00 3.72
2700 2715 1.141665 GGGGCCGATGCAATTGTTC 59.858 57.895 7.40 4.06 40.13 3.18
2762 2777 3.608316 AGTGCTCTTTTCCTGCTCTAG 57.392 47.619 0.00 0.00 0.00 2.43
2823 2838 4.875544 TTAGAAATGCTACCAACATCGC 57.124 40.909 0.00 0.00 0.00 4.58
2837 2852 9.515020 CTACCAACATCGCAATATGTTTTATTT 57.485 29.630 6.38 0.00 45.54 1.40
2868 2883 9.140286 TGACATTCGTAGATACTTCTTTTTCTG 57.860 33.333 0.00 0.00 35.04 3.02
2913 2928 7.225784 TGATATTAGGTGCATTTGTGTGTTT 57.774 32.000 0.00 0.00 0.00 2.83
2962 2977 6.704289 ACCTGGAATTCATGTCATTGTATG 57.296 37.500 7.93 0.00 0.00 2.39
2982 2997 1.678101 GTGCTGCTCACTCAAGGTTTT 59.322 47.619 0.00 0.00 42.38 2.43
3228 3243 1.615384 GCTGAGCTTCCTGATTGGGTT 60.615 52.381 0.00 0.00 36.20 4.11
3231 3246 2.642311 TGAGCTTCCTGATTGGGTTGTA 59.358 45.455 0.00 0.00 36.20 2.41
3258 3273 2.885135 TCCCAGTGCTGATGTCATTT 57.115 45.000 0.02 0.00 0.00 2.32
3264 3279 5.359009 CCCAGTGCTGATGTCATTTCTAAAT 59.641 40.000 0.02 0.00 0.00 1.40
3285 3300 2.361104 GCCCCTGCACCGAAATCA 60.361 61.111 0.00 0.00 37.47 2.57
3330 3345 2.610479 GCTCTTCGAGAACACCATGTCA 60.610 50.000 0.00 0.00 0.00 3.58
3396 3411 1.134699 AGCACATATGAGTGGGTCGTG 60.135 52.381 10.38 0.00 39.87 4.35
3426 3441 2.595754 GGCCGATCATTGGAGGGC 60.596 66.667 0.00 0.00 42.71 5.19
3447 3462 0.034186 ATCTCATTTCCTTGGCGCCA 60.034 50.000 29.03 29.03 0.00 5.69
3468 3483 4.501400 CCAAAGGGGTTGAAGCAACTAAAG 60.501 45.833 9.80 0.00 43.14 1.85
3480 3495 4.911390 AGCAACTAAAGTATGGCTCAGTT 58.089 39.130 0.00 0.00 0.00 3.16
3624 3639 5.681337 GCTTACTATCAAAGCAAGGGATC 57.319 43.478 3.07 0.00 46.85 3.36
3640 3655 3.137360 AGGGATCCACTTCTATTTCCTGC 59.863 47.826 15.23 0.00 0.00 4.85
3816 3831 0.537828 GTAGGAGCTAGGACCCCGAG 60.538 65.000 0.00 0.00 0.00 4.63
3917 3932 5.471116 TCATCTTGTTGTTCTGTGAATCTGG 59.529 40.000 0.00 0.00 0.00 3.86
3931 3946 3.753272 TGAATCTGGCTAACTGTTTCTGC 59.247 43.478 0.00 1.52 31.67 4.26
3932 3947 2.185004 TCTGGCTAACTGTTTCTGCC 57.815 50.000 18.47 18.47 43.49 4.85
3933 3948 1.699634 TCTGGCTAACTGTTTCTGCCT 59.300 47.619 22.66 0.00 43.57 4.75
3934 3949 2.106511 TCTGGCTAACTGTTTCTGCCTT 59.893 45.455 22.66 0.00 43.57 4.35
3935 3950 2.887152 CTGGCTAACTGTTTCTGCCTTT 59.113 45.455 22.66 0.00 43.57 3.11
3936 3951 2.884639 TGGCTAACTGTTTCTGCCTTTC 59.115 45.455 22.66 6.65 43.57 2.62
3937 3952 3.149981 GGCTAACTGTTTCTGCCTTTCT 58.850 45.455 18.20 0.00 40.36 2.52
3938 3953 3.057946 GGCTAACTGTTTCTGCCTTTCTG 60.058 47.826 18.20 0.00 40.36 3.02
4060 4075 1.726248 TCAGTTGTGTTGATCGATGCG 59.274 47.619 0.54 0.00 0.00 4.73
4075 4090 3.310774 TCGATGCGTCTGTTAGTACCTAC 59.689 47.826 4.05 0.00 0.00 3.18
4108 4123 5.181690 TCGTCAAAAGCTTGCTACATTTT 57.818 34.783 0.00 0.00 32.14 1.82
4123 4138 7.153315 TGCTACATTTTTGCATCATCTCAAAA 58.847 30.769 0.00 0.00 39.53 2.44
4142 4157 8.784043 TCTCAAAATTCCACTCTAAAAAGTAGC 58.216 33.333 0.00 0.00 0.00 3.58
4171 4186 5.708697 TGACTAGAACTGACGAGTAATTCCA 59.291 40.000 0.00 0.00 0.00 3.53
4173 4188 6.565234 ACTAGAACTGACGAGTAATTCCATG 58.435 40.000 0.00 0.00 0.00 3.66
4174 4189 4.759782 AGAACTGACGAGTAATTCCATGG 58.240 43.478 4.97 4.97 0.00 3.66
4183 4198 5.470098 ACGAGTAATTCCATGGCATACAATC 59.530 40.000 6.96 1.74 0.00 2.67
4194 4209 5.389859 TGGCATACAATCTGAAGTTTTGG 57.610 39.130 0.00 0.00 0.00 3.28
4196 4211 4.082026 GGCATACAATCTGAAGTTTTGGCT 60.082 41.667 11.60 0.00 0.00 4.75
4260 7721 4.351874 AGATGATACCATTTACACCCGG 57.648 45.455 0.00 0.00 32.09 5.73
4264 7725 0.542805 TACCATTTACACCCGGCCTC 59.457 55.000 0.00 0.00 0.00 4.70
4281 7742 2.945668 GCCTCTGGGACAACACAATATC 59.054 50.000 0.00 0.00 38.70 1.63
4283 7744 4.785301 CCTCTGGGACAACACAATATCAT 58.215 43.478 0.00 0.00 38.70 2.45
4289 7750 4.949856 GGGACAACACAATATCATGACCTT 59.050 41.667 0.00 0.00 0.00 3.50
4301 7762 2.825532 TCATGACCTTGTCGAGACATCA 59.174 45.455 6.77 8.38 41.52 3.07
4303 7764 3.744238 TGACCTTGTCGAGACATCAAA 57.256 42.857 6.77 0.00 41.52 2.69
4325 7788 1.781786 TGCACAACTAAAAAGGGCCA 58.218 45.000 6.18 0.00 0.00 5.36
4350 7813 4.584327 AAACCAAGGACTTGCAACATAC 57.416 40.909 6.54 0.00 39.16 2.39
4365 7828 4.414852 CAACATACAAGCAGTAATGCCAC 58.585 43.478 12.26 0.00 36.05 5.01
4378 7841 0.107508 ATGCCACTCATCGTCCTTGG 60.108 55.000 0.00 0.00 0.00 3.61
4435 7905 2.943653 GACCCGTCCTTGCGTTTG 59.056 61.111 0.00 0.00 0.00 2.93
4436 7906 2.593436 ACCCGTCCTTGCGTTTGG 60.593 61.111 0.00 0.00 0.00 3.28
4447 7917 5.980715 GTCCTTGCGTTTGGATTTTTCTTAA 59.019 36.000 0.00 0.00 34.58 1.85
4457 7927 9.114952 GTTTGGATTTTTCTTAAAATTGGTCCA 57.885 29.630 0.00 0.00 42.51 4.02
4469 7939 1.130678 TTGGTCCAAATTTGGCCCCC 61.131 55.000 29.63 25.97 45.67 5.40
4483 7953 1.115326 GCCCCCAAACCAGATATGGC 61.115 60.000 6.21 0.00 32.71 4.40
4486 7956 0.261402 CCCAAACCAGATATGGCCCA 59.739 55.000 6.21 0.00 32.71 5.36
4500 7970 1.368579 GCCCATTGTGCAAGCTGTT 59.631 52.632 0.00 0.00 0.00 3.16
4501 7971 0.602562 GCCCATTGTGCAAGCTGTTA 59.397 50.000 0.00 0.00 0.00 2.41
4508 7978 0.453390 GTGCAAGCTGTTAGCCCATC 59.547 55.000 0.00 0.00 43.77 3.51
4511 7981 1.957113 GCAAGCTGTTAGCCCATCCTT 60.957 52.381 0.00 0.00 43.77 3.36
4512 7982 2.683742 GCAAGCTGTTAGCCCATCCTTA 60.684 50.000 0.00 0.00 43.77 2.69
4523 7993 0.318762 CCATCCTTAGCCCGCTCTAC 59.681 60.000 0.00 0.00 0.00 2.59
4544 8014 0.960364 ATTTCCATCGCGTTGTGCCT 60.960 50.000 15.50 0.00 42.08 4.75
4546 8016 2.434884 CCATCGCGTTGTGCCTCT 60.435 61.111 15.50 0.00 42.08 3.69
4547 8017 2.456119 CCATCGCGTTGTGCCTCTC 61.456 63.158 15.50 0.00 42.08 3.20
4548 8018 1.446792 CATCGCGTTGTGCCTCTCT 60.447 57.895 5.77 0.00 42.08 3.10
4559 8029 1.296068 GCCTCTCTGCTTGAGTGCT 59.704 57.895 7.08 0.00 43.13 4.40
4566 8036 2.352034 CTCTGCTTGAGTGCTGCTATTG 59.648 50.000 0.00 0.00 37.99 1.90
4567 8037 2.027837 TCTGCTTGAGTGCTGCTATTGA 60.028 45.455 0.00 0.00 32.95 2.57
4568 8038 2.352034 CTGCTTGAGTGCTGCTATTGAG 59.648 50.000 0.00 0.00 0.00 3.02
4569 8039 1.669779 GCTTGAGTGCTGCTATTGAGG 59.330 52.381 0.00 0.00 0.00 3.86
4570 8040 2.286872 CTTGAGTGCTGCTATTGAGGG 58.713 52.381 0.00 0.00 0.00 4.30
4571 8041 1.571955 TGAGTGCTGCTATTGAGGGA 58.428 50.000 0.00 0.00 0.00 4.20
4572 8042 2.121948 TGAGTGCTGCTATTGAGGGAT 58.878 47.619 0.00 0.00 0.00 3.85
4573 8043 2.507058 TGAGTGCTGCTATTGAGGGATT 59.493 45.455 0.00 0.00 0.00 3.01
4574 8044 3.137533 GAGTGCTGCTATTGAGGGATTC 58.862 50.000 0.00 0.00 0.00 2.52
4575 8045 2.507058 AGTGCTGCTATTGAGGGATTCA 59.493 45.455 0.00 0.00 0.00 2.57
4576 8046 2.877168 GTGCTGCTATTGAGGGATTCAG 59.123 50.000 0.00 0.00 37.07 3.02
4577 8047 1.878734 GCTGCTATTGAGGGATTCAGC 59.121 52.381 0.00 0.00 37.07 4.26
4578 8048 2.502295 CTGCTATTGAGGGATTCAGCC 58.498 52.381 0.00 0.00 37.07 4.85
4579 8049 1.845791 TGCTATTGAGGGATTCAGCCA 59.154 47.619 0.00 0.00 37.07 4.75
4580 8050 2.225467 GCTATTGAGGGATTCAGCCAC 58.775 52.381 0.00 0.00 37.07 5.01
4581 8051 2.856222 CTATTGAGGGATTCAGCCACC 58.144 52.381 0.00 0.00 37.07 4.61
4582 8052 0.107017 ATTGAGGGATTCAGCCACCG 60.107 55.000 0.00 0.00 37.07 4.94
4583 8053 1.488705 TTGAGGGATTCAGCCACCGT 61.489 55.000 0.00 0.00 37.07 4.83
4584 8054 1.299976 GAGGGATTCAGCCACCGTT 59.700 57.895 0.00 0.00 0.00 4.44
4585 8055 1.002134 AGGGATTCAGCCACCGTTG 60.002 57.895 0.00 0.00 0.00 4.10
4586 8056 1.303317 GGGATTCAGCCACCGTTGT 60.303 57.895 0.00 0.00 0.00 3.32
4587 8057 1.305930 GGGATTCAGCCACCGTTGTC 61.306 60.000 0.00 0.00 0.00 3.18
4588 8058 1.635663 GGATTCAGCCACCGTTGTCG 61.636 60.000 0.00 0.00 0.00 4.35
4600 8070 2.667473 CGTTGTCGGAAATACTCCCT 57.333 50.000 0.00 0.00 41.87 4.20
4601 8071 2.537401 CGTTGTCGGAAATACTCCCTC 58.463 52.381 0.00 0.00 41.87 4.30
4602 8072 2.737679 CGTTGTCGGAAATACTCCCTCC 60.738 54.545 0.00 0.00 41.87 4.30
4603 8073 2.235402 GTTGTCGGAAATACTCCCTCCA 59.765 50.000 0.00 0.00 41.87 3.86
4604 8074 2.759355 TGTCGGAAATACTCCCTCCAT 58.241 47.619 0.00 0.00 41.87 3.41
4605 8075 3.112263 TGTCGGAAATACTCCCTCCATT 58.888 45.455 0.00 0.00 41.87 3.16
4606 8076 3.134081 TGTCGGAAATACTCCCTCCATTC 59.866 47.826 0.00 0.00 41.87 2.67
4607 8077 2.704065 TCGGAAATACTCCCTCCATTCC 59.296 50.000 0.00 0.00 41.87 3.01
4608 8078 2.438021 CGGAAATACTCCCTCCATTCCA 59.562 50.000 0.00 0.00 41.87 3.53
4609 8079 3.073062 CGGAAATACTCCCTCCATTCCAT 59.927 47.826 0.00 0.00 41.87 3.41
4610 8080 4.286032 CGGAAATACTCCCTCCATTCCATA 59.714 45.833 0.00 0.00 41.87 2.74
4611 8081 5.045578 CGGAAATACTCCCTCCATTCCATAT 60.046 44.000 0.00 0.00 41.87 1.78
4612 8082 6.522459 CGGAAATACTCCCTCCATTCCATATT 60.522 42.308 0.00 0.00 41.87 1.28
4613 8083 7.311046 CGGAAATACTCCCTCCATTCCATATTA 60.311 40.741 0.00 0.00 41.87 0.98
4614 8084 7.829706 GGAAATACTCCCTCCATTCCATATTAC 59.170 40.741 0.00 0.00 38.44 1.89
4615 8085 8.525729 AAATACTCCCTCCATTCCATATTACT 57.474 34.615 0.00 0.00 0.00 2.24
4616 8086 8.525729 AATACTCCCTCCATTCCATATTACTT 57.474 34.615 0.00 0.00 0.00 2.24
4617 8087 6.192970 ACTCCCTCCATTCCATATTACTTG 57.807 41.667 0.00 0.00 0.00 3.16
4618 8088 5.672194 ACTCCCTCCATTCCATATTACTTGT 59.328 40.000 0.00 0.00 0.00 3.16
4619 8089 6.183361 ACTCCCTCCATTCCATATTACTTGTC 60.183 42.308 0.00 0.00 0.00 3.18
4620 8090 4.997395 CCCTCCATTCCATATTACTTGTCG 59.003 45.833 0.00 0.00 0.00 4.35
4621 8091 4.452455 CCTCCATTCCATATTACTTGTCGC 59.548 45.833 0.00 0.00 0.00 5.19
4622 8092 5.290493 TCCATTCCATATTACTTGTCGCT 57.710 39.130 0.00 0.00 0.00 4.93
4623 8093 5.056480 TCCATTCCATATTACTTGTCGCTG 58.944 41.667 0.00 0.00 0.00 5.18
4624 8094 5.056480 CCATTCCATATTACTTGTCGCTGA 58.944 41.667 0.00 0.00 0.00 4.26
4625 8095 5.702670 CCATTCCATATTACTTGTCGCTGAT 59.297 40.000 0.00 0.00 0.00 2.90
4626 8096 6.205464 CCATTCCATATTACTTGTCGCTGATT 59.795 38.462 0.00 0.00 0.00 2.57
4627 8097 7.255242 CCATTCCATATTACTTGTCGCTGATTT 60.255 37.037 0.00 0.00 0.00 2.17
4628 8098 8.773645 CATTCCATATTACTTGTCGCTGATTTA 58.226 33.333 0.00 0.00 0.00 1.40
4629 8099 7.946655 TCCATATTACTTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
4630 8100 7.497595 TCCATATTACTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
4631 8101 8.635328 TCCATATTACTTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
4632 8102 8.700644 CCATATTACTTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
4633 8103 9.244799 CATATTACTTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
4634 8104 9.811995 ATATTACTTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 34.99 2.41
4635 8105 7.949903 TTACTTGTCGCTGATTTAGTACAAA 57.050 32.000 0.00 0.00 35.46 2.83
4636 8106 6.467723 ACTTGTCGCTGATTTAGTACAAAG 57.532 37.500 0.00 0.00 35.46 2.77
4637 8107 5.989777 ACTTGTCGCTGATTTAGTACAAAGT 59.010 36.000 0.00 0.00 35.46 2.66
4638 8108 6.482308 ACTTGTCGCTGATTTAGTACAAAGTT 59.518 34.615 0.00 0.00 35.46 2.66
4639 8109 6.223138 TGTCGCTGATTTAGTACAAAGTTG 57.777 37.500 0.00 0.00 0.00 3.16
4640 8110 5.756347 TGTCGCTGATTTAGTACAAAGTTGT 59.244 36.000 1.75 1.75 44.86 3.32
4641 8111 6.924612 TGTCGCTGATTTAGTACAAAGTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
4642 8112 7.601130 TGTCGCTGATTTAGTACAAAGTTGTAT 59.399 33.333 7.14 0.74 44.59 2.29
4643 8113 8.440833 GTCGCTGATTTAGTACAAAGTTGTATT 58.559 33.333 7.14 5.91 44.59 1.89
4644 8114 9.642327 TCGCTGATTTAGTACAAAGTTGTATTA 57.358 29.630 7.14 4.99 44.59 0.98
4653 8123 8.542497 AGTACAAAGTTGTATTAAATCAGCGA 57.458 30.769 7.14 0.00 44.59 4.93
4654 8124 8.440833 AGTACAAAGTTGTATTAAATCAGCGAC 58.559 33.333 7.14 0.00 44.59 5.19
4655 8125 7.197071 ACAAAGTTGTATTAAATCAGCGACA 57.803 32.000 0.00 0.00 40.16 4.35
4656 8126 7.644490 ACAAAGTTGTATTAAATCAGCGACAA 58.356 30.769 0.00 0.00 40.16 3.18
4657 8127 7.803189 ACAAAGTTGTATTAAATCAGCGACAAG 59.197 33.333 0.00 0.00 40.16 3.16
4658 8128 7.435068 AAGTTGTATTAAATCAGCGACAAGT 57.565 32.000 0.00 0.00 33.10 3.16
4659 8129 8.542497 AAGTTGTATTAAATCAGCGACAAGTA 57.458 30.769 0.00 0.00 31.84 2.24
4660 8130 8.542497 AGTTGTATTAAATCAGCGACAAGTAA 57.458 30.769 0.00 0.00 30.66 2.24
4661 8131 9.162764 AGTTGTATTAAATCAGCGACAAGTAAT 57.837 29.630 0.00 0.00 30.66 1.89
4666 8136 8.902540 ATTAAATCAGCGACAAGTAATATGGA 57.097 30.769 0.00 0.00 0.00 3.41
4667 8137 8.725405 TTAAATCAGCGACAAGTAATATGGAA 57.275 30.769 0.00 0.00 0.00 3.53
4668 8138 6.604735 AATCAGCGACAAGTAATATGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
4688 8158 8.195165 TGGAACAGAGGATGTATATCTTTAGG 57.805 38.462 0.00 0.00 43.00 2.69
4689 8159 7.100409 GGAACAGAGGATGTATATCTTTAGGC 58.900 42.308 0.00 0.00 43.00 3.93
4690 8160 7.256332 GGAACAGAGGATGTATATCTTTAGGCA 60.256 40.741 0.00 0.00 43.00 4.75
4691 8161 6.998802 ACAGAGGATGTATATCTTTAGGCAC 58.001 40.000 0.00 0.00 41.60 5.01
4692 8162 6.014156 ACAGAGGATGTATATCTTTAGGCACC 60.014 42.308 0.00 0.00 41.60 5.01
4693 8163 6.014242 CAGAGGATGTATATCTTTAGGCACCA 60.014 42.308 0.00 0.00 33.68 4.17
4694 8164 6.014156 AGAGGATGTATATCTTTAGGCACCAC 60.014 42.308 0.00 0.00 33.68 4.16
4695 8165 5.013183 AGGATGTATATCTTTAGGCACCACC 59.987 44.000 0.00 0.00 34.27 4.61
4696 8166 5.221843 GGATGTATATCTTTAGGCACCACCA 60.222 44.000 0.00 0.00 35.61 4.17
4697 8167 5.904984 TGTATATCTTTAGGCACCACCAT 57.095 39.130 0.00 0.00 43.14 3.55
4698 8168 5.865085 TGTATATCTTTAGGCACCACCATC 58.135 41.667 0.00 0.00 43.14 3.51
4699 8169 2.332063 ATCTTTAGGCACCACCATCG 57.668 50.000 0.00 0.00 43.14 3.84
4700 8170 0.392461 TCTTTAGGCACCACCATCGC 60.392 55.000 0.00 0.00 43.14 4.58
4701 8171 1.705337 CTTTAGGCACCACCATCGCG 61.705 60.000 0.00 0.00 43.14 5.87
4702 8172 2.457743 TTTAGGCACCACCATCGCGT 62.458 55.000 5.77 0.00 43.14 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
389 390 9.547279 TCCAACTATCCTCTATAAATAGCATCA 57.453 33.333 0.00 0.00 0.00 3.07
422 423 9.656040 TGTATTCAATTTACTTTAGTTCCGCTA 57.344 29.630 0.00 0.00 0.00 4.26
507 508 5.321102 AGAGCACTCTTCTCAACTCTTCTA 58.679 41.667 0.00 0.00 36.31 2.10
508 509 4.151883 AGAGCACTCTTCTCAACTCTTCT 58.848 43.478 0.00 0.00 36.31 2.85
509 510 4.519540 AGAGCACTCTTCTCAACTCTTC 57.480 45.455 0.00 0.00 36.31 2.87
510 511 5.321102 TCTAGAGCACTCTTCTCAACTCTT 58.679 41.667 5.33 0.00 40.93 2.85
511 512 4.917385 TCTAGAGCACTCTTCTCAACTCT 58.083 43.478 5.33 0.00 40.93 3.24
512 513 5.835113 ATCTAGAGCACTCTTCTCAACTC 57.165 43.478 5.33 0.00 40.93 3.01
513 514 6.184068 TGTATCTAGAGCACTCTTCTCAACT 58.816 40.000 5.33 0.00 40.93 3.16
514 515 6.443934 TGTATCTAGAGCACTCTTCTCAAC 57.556 41.667 5.33 0.20 40.93 3.18
515 516 6.017523 CGATGTATCTAGAGCACTCTTCTCAA 60.018 42.308 5.33 0.00 40.93 3.02
516 517 5.468409 CGATGTATCTAGAGCACTCTTCTCA 59.532 44.000 5.33 0.38 40.93 3.27
517 518 5.616866 GCGATGTATCTAGAGCACTCTTCTC 60.617 48.000 5.33 0.00 40.93 2.87
541 552 3.185246 AGCACAATCTATGGTCCTTCG 57.815 47.619 0.00 0.00 0.00 3.79
567 578 1.077716 GTCATGTACCCCTGGTGCC 60.078 63.158 0.00 0.00 37.51 5.01
593 604 0.037605 CACTTGGTGGGGAGTCGTAC 60.038 60.000 0.00 0.00 0.00 3.67
642 653 5.523916 CCTCATTACCGACCAGTGATTTTAG 59.476 44.000 0.00 0.00 0.00 1.85
669 680 3.196463 TCCGTTTAAAGTTGAAGCACGA 58.804 40.909 0.00 0.00 0.00 4.35
811 823 2.343758 CCACCACTCCACTCCGTG 59.656 66.667 0.00 0.00 0.00 4.94
814 826 2.147387 ACCACCACCACTCCACTCC 61.147 63.158 0.00 0.00 0.00 3.85
993 1005 2.133281 TCCATGGTGCCATCAAAGAG 57.867 50.000 12.58 0.00 33.90 2.85
1107 1120 1.519455 GCCACCGTTGATCTCCGAG 60.519 63.158 6.22 0.00 0.00 4.63
1167 1180 1.079057 GTTCTTCACCCTCCGCCTC 60.079 63.158 0.00 0.00 0.00 4.70
1246 1259 4.827087 CGCAGCGGATGTGAGCCT 62.827 66.667 7.00 0.00 42.31 4.58
1324 1337 1.895707 CCTCGCATTCCCCATCAGC 60.896 63.158 0.00 0.00 0.00 4.26
1460 1473 1.480954 TGAAGATAGCGAGGTTCACCC 59.519 52.381 0.00 0.00 36.42 4.61
1463 1476 4.736126 TTGATGAAGATAGCGAGGTTCA 57.264 40.909 0.00 0.00 33.61 3.18
1474 1487 7.206981 ACGTGTTGAAAGAATTGATGAAGAT 57.793 32.000 0.00 0.00 0.00 2.40
1666 1679 2.191641 GGGGTCCTCTGCATCAGC 59.808 66.667 0.00 0.00 42.57 4.26
1747 1760 0.107831 TTGTAGGTGGTGGCAGTGAC 59.892 55.000 0.00 0.00 0.00 3.67
1748 1761 1.064003 ATTGTAGGTGGTGGCAGTGA 58.936 50.000 0.00 0.00 0.00 3.41
1810 1825 6.585695 ACACCTAAATAGAACAAGAGACGA 57.414 37.500 0.00 0.00 0.00 4.20
1811 1826 7.376336 CGATACACCTAAATAGAACAAGAGACG 59.624 40.741 0.00 0.00 0.00 4.18
1812 1827 7.648510 CCGATACACCTAAATAGAACAAGAGAC 59.351 40.741 0.00 0.00 0.00 3.36
1853 1868 2.223572 CGGCCAATCTAAATTGCAGACC 60.224 50.000 2.24 0.00 40.85 3.85
1901 1916 1.645704 CCACGTCATCGGAGTCGTCT 61.646 60.000 0.00 0.00 41.85 4.18
1925 1940 3.371273 CCTCCTCTTTGATCAATGCCTGA 60.371 47.826 9.40 7.76 38.81 3.86
1943 1958 1.904990 GCCTCCACTTCTCCACCTCC 61.905 65.000 0.00 0.00 0.00 4.30
2129 2144 5.770162 AGAACTGAACTCCACCTTAAAATGG 59.230 40.000 0.00 0.00 37.32 3.16
2144 2159 7.865707 ACATTCACATACTTCAAGAACTGAAC 58.134 34.615 0.00 0.00 39.20 3.18
2240 2255 0.107508 ATGACCATCTGGCTTGGACG 60.108 55.000 8.38 0.00 39.32 4.79
2375 2390 1.918293 CCTCCACACCCCAGCTGTA 60.918 63.158 13.81 0.00 0.00 2.74
2402 2417 2.055042 CCCTCCTGAGTCCTCCACG 61.055 68.421 0.00 0.00 0.00 4.94
2462 2477 2.332654 GCCCTTTAGGTGTGCACGG 61.333 63.158 13.13 5.55 38.26 4.94
2498 2513 4.082408 ACAAGATGCACCTCAACATCATTG 60.082 41.667 5.84 8.79 44.16 2.82
2588 2603 8.618677 CAGAGATGACACACAAATTAGCATAAT 58.381 33.333 0.00 0.00 0.00 1.28
2622 2637 3.186909 CGACTCTGGTAATTCGCATTGA 58.813 45.455 0.00 0.00 0.00 2.57
2837 2852 7.392494 AGAAGTATCTACGAATGTCACAAGA 57.608 36.000 0.00 0.00 32.88 3.02
2849 2864 8.535690 AAAGTCCAGAAAAAGAAGTATCTACG 57.464 34.615 0.00 0.00 33.77 3.51
2982 2997 4.264460 AGCCGGCATAATCAAAAACAAA 57.736 36.364 31.54 0.00 0.00 2.83
3030 3045 6.621596 GCAGTACCTTGCTATCTTTGACAAAG 60.622 42.308 19.93 19.93 40.89 2.77
3048 3063 5.786264 TTAGCTACCATTAGAGCAGTACC 57.214 43.478 0.00 0.00 41.36 3.34
3102 3117 5.198602 AGAAAAGGAATATCAGGTTGGCT 57.801 39.130 0.00 0.00 0.00 4.75
3228 3243 3.517500 TCAGCACTGGGATGTAACATACA 59.482 43.478 0.00 0.00 43.80 2.29
3231 3246 3.548770 CATCAGCACTGGGATGTAACAT 58.451 45.455 0.00 0.00 36.89 2.71
3285 3300 4.601857 AGGTATGGGATGATAAACGGGAAT 59.398 41.667 0.00 0.00 0.00 3.01
3330 3345 4.406456 TCATGGCATTGAACTTGGTAACT 58.594 39.130 0.00 0.00 37.61 2.24
3396 3411 2.240162 ATCGGCCGGACTTCTTGGTC 62.240 60.000 27.83 0.00 35.66 4.02
3408 3423 2.281070 CCCTCCAATGATCGGCCG 60.281 66.667 22.12 22.12 0.00 6.13
3426 3441 0.305922 GCGCCAAGGAAATGAGATCG 59.694 55.000 0.00 0.00 0.00 3.69
3447 3462 4.286707 ACTTTAGTTGCTTCAACCCCTTT 58.713 39.130 6.12 0.00 44.49 3.11
3480 3495 0.323302 TTGCTACGTTGATGGCTGGA 59.677 50.000 0.00 0.00 0.00 3.86
3624 3639 3.691609 GGAACAGCAGGAAATAGAAGTGG 59.308 47.826 0.00 0.00 0.00 4.00
3816 3831 4.557605 CCATGCCGCATGTTCGCC 62.558 66.667 27.48 0.00 39.94 5.54
3886 3901 6.650807 TCACAGAACAACAAGATGACTAATCC 59.349 38.462 0.00 0.00 35.72 3.01
3890 3905 7.386025 CAGATTCACAGAACAACAAGATGACTA 59.614 37.037 0.00 0.00 0.00 2.59
3904 3919 4.623932 ACAGTTAGCCAGATTCACAGAA 57.376 40.909 0.00 0.00 0.00 3.02
3917 3932 3.057946 CCAGAAAGGCAGAAACAGTTAGC 60.058 47.826 0.00 0.00 0.00 3.09
3931 3946 5.972107 AAGAATGTGATTGACCAGAAAGG 57.028 39.130 0.00 0.00 45.67 3.11
3932 3947 7.205297 ACAAAAGAATGTGATTGACCAGAAAG 58.795 34.615 0.00 0.00 30.82 2.62
3933 3948 7.111247 ACAAAAGAATGTGATTGACCAGAAA 57.889 32.000 0.00 0.00 30.82 2.52
3934 3949 6.713762 ACAAAAGAATGTGATTGACCAGAA 57.286 33.333 0.00 0.00 30.82 3.02
3935 3950 7.284261 TGTTACAAAAGAATGTGATTGACCAGA 59.716 33.333 0.00 0.00 34.75 3.86
3936 3951 7.424803 TGTTACAAAAGAATGTGATTGACCAG 58.575 34.615 0.00 0.00 34.75 4.00
3937 3952 7.340122 TGTTACAAAAGAATGTGATTGACCA 57.660 32.000 0.00 0.00 34.75 4.02
3938 3953 7.867403 ACATGTTACAAAAGAATGTGATTGACC 59.133 33.333 0.00 0.00 34.75 4.02
4006 4021 7.290248 TCGGGAAATCATATCTATAGGGGATTC 59.710 40.741 0.00 0.00 0.00 2.52
4016 4031 6.494666 AACAAGGTCGGGAAATCATATCTA 57.505 37.500 0.00 0.00 0.00 1.98
4020 4035 4.912586 TGAAACAAGGTCGGGAAATCATA 58.087 39.130 0.00 0.00 0.00 2.15
4108 4123 5.713389 AGAGTGGAATTTTGAGATGATGCAA 59.287 36.000 0.00 0.00 0.00 4.08
4123 4138 5.560724 TGCAGCTACTTTTTAGAGTGGAAT 58.439 37.500 0.00 0.00 30.45 3.01
4142 4157 3.119673 ACTCGTCAGTTCTAGTCATGCAG 60.120 47.826 0.00 0.00 0.00 4.41
4171 4186 5.625197 GCCAAAACTTCAGATTGTATGCCAT 60.625 40.000 0.00 0.00 0.00 4.40
4173 4188 4.082026 AGCCAAAACTTCAGATTGTATGCC 60.082 41.667 0.00 0.00 0.00 4.40
4174 4189 5.064441 AGCCAAAACTTCAGATTGTATGC 57.936 39.130 0.00 0.00 0.00 3.14
4183 4198 7.826260 TTTTTGAAACTAGCCAAAACTTCAG 57.174 32.000 14.12 0.00 40.60 3.02
4233 4252 8.932791 CGGGTGTAAATGGTATCATCTTAATAC 58.067 37.037 0.00 0.00 32.24 1.89
4251 7712 3.006728 CCCAGAGGCCGGGTGTAA 61.007 66.667 2.18 0.00 39.05 2.41
4260 7721 2.489938 TATTGTGTTGTCCCAGAGGC 57.510 50.000 0.00 0.00 0.00 4.70
4264 7725 4.336433 GGTCATGATATTGTGTTGTCCCAG 59.664 45.833 0.00 0.00 0.00 4.45
4281 7742 3.236632 TGATGTCTCGACAAGGTCATG 57.763 47.619 3.60 0.00 45.41 3.07
4283 7744 3.320826 TCTTTGATGTCTCGACAAGGTCA 59.679 43.478 3.60 1.16 45.41 4.02
4289 7750 2.995939 GTGCATCTTTGATGTCTCGACA 59.004 45.455 1.79 1.79 46.44 4.35
4301 7762 4.503123 GGCCCTTTTTAGTTGTGCATCTTT 60.503 41.667 0.00 0.00 0.00 2.52
4303 7764 2.562738 GGCCCTTTTTAGTTGTGCATCT 59.437 45.455 0.00 0.00 0.00 2.90
4325 7788 3.007398 TGTTGCAAGTCCTTGGTTTTGTT 59.993 39.130 0.00 0.00 40.74 2.83
4365 7828 1.081892 CTGTTGCCAAGGACGATGAG 58.918 55.000 0.00 0.00 0.00 2.90
4378 7841 3.248446 TACCCTCGGTGCCTGTTGC 62.248 63.158 0.00 0.00 36.19 4.17
4386 7849 3.066190 TCGCCACTACCCTCGGTG 61.066 66.667 0.00 0.00 36.19 4.94
4388 7851 3.834799 GGTCGCCACTACCCTCGG 61.835 72.222 0.00 0.00 0.00 4.63
4389 7852 2.162338 TTTGGTCGCCACTACCCTCG 62.162 60.000 0.00 0.00 36.06 4.63
4430 7900 8.279800 GGACCAATTTTAAGAAAAATCCAAACG 58.720 33.333 0.00 0.00 43.04 3.60
4466 7936 0.469892 GGGCCATATCTGGTTTGGGG 60.470 60.000 4.39 0.00 45.10 4.96
4469 7939 3.033184 ACAATGGGCCATATCTGGTTTG 58.967 45.455 21.54 14.75 45.10 2.93
4472 7942 1.755265 GCACAATGGGCCATATCTGGT 60.755 52.381 21.54 10.37 45.10 4.00
4476 7946 1.269936 GCTTGCACAATGGGCCATATC 60.270 52.381 21.54 9.64 0.00 1.63
4483 7953 1.403249 GCTAACAGCTTGCACAATGGG 60.403 52.381 0.00 0.00 38.45 4.00
4486 7956 0.890683 GGGCTAACAGCTTGCACAAT 59.109 50.000 0.00 0.00 41.99 2.71
4500 7970 2.516888 GCGGGCTAAGGATGGGCTA 61.517 63.158 0.00 0.00 32.78 3.93
4501 7971 3.878667 GCGGGCTAAGGATGGGCT 61.879 66.667 0.00 0.00 32.78 5.19
4508 7978 0.674534 AATCGTAGAGCGGGCTAAGG 59.325 55.000 0.00 0.00 43.63 2.69
4511 7981 0.672342 GGAAATCGTAGAGCGGGCTA 59.328 55.000 0.00 0.00 43.63 3.93
4512 7982 1.327690 TGGAAATCGTAGAGCGGGCT 61.328 55.000 0.00 0.00 43.63 5.19
4523 7993 0.857311 GCACAACGCGATGGAAATCG 60.857 55.000 20.87 3.81 45.99 3.34
4534 8004 1.963338 AAGCAGAGAGGCACAACGC 60.963 57.895 0.00 0.00 41.28 4.84
4546 8016 2.027837 TCAATAGCAGCACTCAAGCAGA 60.028 45.455 0.00 0.00 36.85 4.26
4547 8017 2.352034 CTCAATAGCAGCACTCAAGCAG 59.648 50.000 0.00 0.00 36.85 4.24
4548 8018 2.353323 CTCAATAGCAGCACTCAAGCA 58.647 47.619 0.00 0.00 36.85 3.91
4559 8029 1.845791 TGGCTGAATCCCTCAATAGCA 59.154 47.619 0.00 0.00 32.17 3.49
4566 8036 1.026718 CAACGGTGGCTGAATCCCTC 61.027 60.000 0.00 0.00 0.00 4.30
4567 8037 1.002134 CAACGGTGGCTGAATCCCT 60.002 57.895 0.00 0.00 0.00 4.20
4568 8038 1.303317 ACAACGGTGGCTGAATCCC 60.303 57.895 4.97 0.00 0.00 3.85
4569 8039 1.635663 CGACAACGGTGGCTGAATCC 61.636 60.000 3.96 0.00 35.72 3.01
4570 8040 1.787847 CGACAACGGTGGCTGAATC 59.212 57.895 3.96 0.00 35.72 2.52
4571 8041 3.966215 CGACAACGGTGGCTGAAT 58.034 55.556 3.96 0.00 35.72 2.57
4588 8058 4.731313 ATGGAATGGAGGGAGTATTTCC 57.269 45.455 0.00 0.00 46.00 3.13
4589 8059 8.606830 AGTAATATGGAATGGAGGGAGTATTTC 58.393 37.037 0.00 0.00 0.00 2.17
4590 8060 8.525729 AGTAATATGGAATGGAGGGAGTATTT 57.474 34.615 0.00 0.00 0.00 1.40
4591 8061 8.386264 CAAGTAATATGGAATGGAGGGAGTATT 58.614 37.037 0.00 0.00 0.00 1.89
4592 8062 7.517604 ACAAGTAATATGGAATGGAGGGAGTAT 59.482 37.037 0.00 0.00 0.00 2.12
4593 8063 6.849697 ACAAGTAATATGGAATGGAGGGAGTA 59.150 38.462 0.00 0.00 0.00 2.59
4594 8064 5.672194 ACAAGTAATATGGAATGGAGGGAGT 59.328 40.000 0.00 0.00 0.00 3.85
4595 8065 6.192970 ACAAGTAATATGGAATGGAGGGAG 57.807 41.667 0.00 0.00 0.00 4.30
4596 8066 5.221641 CGACAAGTAATATGGAATGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
4597 8067 4.997395 CGACAAGTAATATGGAATGGAGGG 59.003 45.833 0.00 0.00 0.00 4.30
4598 8068 4.452455 GCGACAAGTAATATGGAATGGAGG 59.548 45.833 0.00 0.00 0.00 4.30
4599 8069 5.178252 CAGCGACAAGTAATATGGAATGGAG 59.822 44.000 0.00 0.00 0.00 3.86
4600 8070 5.056480 CAGCGACAAGTAATATGGAATGGA 58.944 41.667 0.00 0.00 0.00 3.41
4601 8071 5.056480 TCAGCGACAAGTAATATGGAATGG 58.944 41.667 0.00 0.00 0.00 3.16
4602 8072 6.791887 ATCAGCGACAAGTAATATGGAATG 57.208 37.500 0.00 0.00 0.00 2.67
4603 8073 7.807977 AAATCAGCGACAAGTAATATGGAAT 57.192 32.000 0.00 0.00 0.00 3.01
4604 8074 7.985184 ACTAAATCAGCGACAAGTAATATGGAA 59.015 33.333 0.00 0.00 0.00 3.53
4605 8075 7.497595 ACTAAATCAGCGACAAGTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
4606 8076 7.715265 ACTAAATCAGCGACAAGTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
4607 8077 9.244799 TGTACTAAATCAGCGACAAGTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
4608 8078 9.811995 TTGTACTAAATCAGCGACAAGTAATAT 57.188 29.630 0.00 0.00 31.65 1.28
4609 8079 9.642327 TTTGTACTAAATCAGCGACAAGTAATA 57.358 29.630 0.00 0.00 35.77 0.98
4610 8080 8.542497 TTTGTACTAAATCAGCGACAAGTAAT 57.458 30.769 0.00 0.00 35.77 1.89
4611 8081 7.654520 ACTTTGTACTAAATCAGCGACAAGTAA 59.345 33.333 0.00 0.00 35.77 2.24
4612 8082 7.149973 ACTTTGTACTAAATCAGCGACAAGTA 58.850 34.615 0.00 0.00 35.77 2.24
4613 8083 5.989777 ACTTTGTACTAAATCAGCGACAAGT 59.010 36.000 0.00 0.00 35.77 3.16
4614 8084 6.467723 ACTTTGTACTAAATCAGCGACAAG 57.532 37.500 0.00 0.00 35.77 3.16
4615 8085 6.259167 ACAACTTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
4616 8086 5.756347 ACAACTTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
4617 8087 6.224420 ACAACTTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
4618 8088 8.542497 AATACAACTTTGTACTAAATCAGCGA 57.458 30.769 3.95 0.00 45.47 4.93
4627 8097 9.642327 TCGCTGATTTAATACAACTTTGTACTA 57.358 29.630 3.95 0.00 45.47 1.82
4628 8098 8.440833 GTCGCTGATTTAATACAACTTTGTACT 58.559 33.333 3.95 0.00 45.47 2.73
4629 8099 8.225107 TGTCGCTGATTTAATACAACTTTGTAC 58.775 33.333 3.95 0.00 45.47 2.90
4630 8100 8.312896 TGTCGCTGATTTAATACAACTTTGTA 57.687 30.769 4.34 4.34 46.55 2.41
4631 8101 7.197071 TGTCGCTGATTTAATACAACTTTGT 57.803 32.000 0.00 0.00 44.86 2.83
4632 8102 7.803189 ACTTGTCGCTGATTTAATACAACTTTG 59.197 33.333 0.00 0.00 0.00 2.77
4633 8103 7.871853 ACTTGTCGCTGATTTAATACAACTTT 58.128 30.769 0.00 0.00 0.00 2.66
4634 8104 7.435068 ACTTGTCGCTGATTTAATACAACTT 57.565 32.000 0.00 0.00 0.00 2.66
4635 8105 8.542497 TTACTTGTCGCTGATTTAATACAACT 57.458 30.769 0.00 0.00 0.00 3.16
4640 8110 9.990360 TCCATATTACTTGTCGCTGATTTAATA 57.010 29.630 0.00 0.00 0.00 0.98
4641 8111 8.902540 TCCATATTACTTGTCGCTGATTTAAT 57.097 30.769 0.00 0.00 0.00 1.40
4642 8112 8.609176 GTTCCATATTACTTGTCGCTGATTTAA 58.391 33.333 0.00 0.00 0.00 1.52
4643 8113 7.766738 TGTTCCATATTACTTGTCGCTGATTTA 59.233 33.333 0.00 0.00 0.00 1.40
4644 8114 6.597672 TGTTCCATATTACTTGTCGCTGATTT 59.402 34.615 0.00 0.00 0.00 2.17
4645 8115 6.112734 TGTTCCATATTACTTGTCGCTGATT 58.887 36.000 0.00 0.00 0.00 2.57
4646 8116 5.670485 TGTTCCATATTACTTGTCGCTGAT 58.330 37.500 0.00 0.00 0.00 2.90
4647 8117 5.079689 TGTTCCATATTACTTGTCGCTGA 57.920 39.130 0.00 0.00 0.00 4.26
4648 8118 5.109210 TCTGTTCCATATTACTTGTCGCTG 58.891 41.667 0.00 0.00 0.00 5.18
4649 8119 5.339008 TCTGTTCCATATTACTTGTCGCT 57.661 39.130 0.00 0.00 0.00 4.93
4650 8120 4.508124 CCTCTGTTCCATATTACTTGTCGC 59.492 45.833 0.00 0.00 0.00 5.19
4651 8121 5.902681 TCCTCTGTTCCATATTACTTGTCG 58.097 41.667 0.00 0.00 0.00 4.35
4652 8122 7.275920 ACATCCTCTGTTCCATATTACTTGTC 58.724 38.462 0.00 0.00 32.90 3.18
4653 8123 7.200434 ACATCCTCTGTTCCATATTACTTGT 57.800 36.000 0.00 0.00 32.90 3.16
4662 8132 8.820831 CCTAAAGATATACATCCTCTGTTCCAT 58.179 37.037 0.00 0.00 39.39 3.41
4663 8133 7.256332 GCCTAAAGATATACATCCTCTGTTCCA 60.256 40.741 0.00 0.00 39.39 3.53
4664 8134 7.100409 GCCTAAAGATATACATCCTCTGTTCC 58.900 42.308 0.00 0.00 39.39 3.62
4665 8135 7.600752 GTGCCTAAAGATATACATCCTCTGTTC 59.399 40.741 0.00 0.00 39.39 3.18
4666 8136 7.445945 GTGCCTAAAGATATACATCCTCTGTT 58.554 38.462 0.00 0.00 39.39 3.16
4667 8137 6.014156 GGTGCCTAAAGATATACATCCTCTGT 60.014 42.308 0.00 0.00 42.13 3.41
4668 8138 6.014242 TGGTGCCTAAAGATATACATCCTCTG 60.014 42.308 0.00 0.00 0.00 3.35
4669 8139 6.014156 GTGGTGCCTAAAGATATACATCCTCT 60.014 42.308 0.00 0.00 0.00 3.69
4670 8140 6.166982 GTGGTGCCTAAAGATATACATCCTC 58.833 44.000 0.00 0.00 0.00 3.71
4671 8141 5.013183 GGTGGTGCCTAAAGATATACATCCT 59.987 44.000 0.00 0.00 0.00 3.24
4672 8142 5.221843 TGGTGGTGCCTAAAGATATACATCC 60.222 44.000 0.00 0.00 38.35 3.51
4673 8143 5.865085 TGGTGGTGCCTAAAGATATACATC 58.135 41.667 0.00 0.00 38.35 3.06
4674 8144 5.904984 TGGTGGTGCCTAAAGATATACAT 57.095 39.130 0.00 0.00 38.35 2.29
4675 8145 5.510690 CGATGGTGGTGCCTAAAGATATACA 60.511 44.000 0.00 0.00 38.35 2.29
4676 8146 4.929808 CGATGGTGGTGCCTAAAGATATAC 59.070 45.833 0.00 0.00 38.35 1.47
4677 8147 4.562757 GCGATGGTGGTGCCTAAAGATATA 60.563 45.833 0.00 0.00 38.35 0.86
4678 8148 3.807209 GCGATGGTGGTGCCTAAAGATAT 60.807 47.826 0.00 0.00 38.35 1.63
4679 8149 2.484770 GCGATGGTGGTGCCTAAAGATA 60.485 50.000 0.00 0.00 38.35 1.98
4680 8150 1.747206 GCGATGGTGGTGCCTAAAGAT 60.747 52.381 0.00 0.00 38.35 2.40
4681 8151 0.392461 GCGATGGTGGTGCCTAAAGA 60.392 55.000 0.00 0.00 38.35 2.52
4682 8152 1.705337 CGCGATGGTGGTGCCTAAAG 61.705 60.000 0.00 0.00 38.35 1.85
4683 8153 1.743623 CGCGATGGTGGTGCCTAAA 60.744 57.895 0.00 0.00 38.35 1.85
4684 8154 2.125310 CGCGATGGTGGTGCCTAA 60.125 61.111 0.00 0.00 38.35 2.69
4685 8155 3.387091 ACGCGATGGTGGTGCCTA 61.387 61.111 15.93 0.00 38.35 3.93


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

AutoCloner maintained by Alex Coulton.