Multiple sequence alignment - TraesCS1D01G259400

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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 TraesCS1D01G259400 chr1D 100.000 3913 0 0 1 3913 352236299 352232387 0.000000e+00 7227.0
1 TraesCS1D01G259400 chr1A 95.124 2974 117 16 363 3319 452761694 452758732 0.000000e+00 4663.0
2 TraesCS1D01G259400 chr1A 91.608 143 4 6 2 140 452762313 452762175 1.440000e-44 191.0
3 TraesCS1D01G259400 chr1B 93.928 2701 146 9 670 3364 474452053 474449365 0.000000e+00 4063.0
4 TraesCS1D01G259400 chr1B 91.713 362 18 6 4 364 474452724 474452374 3.510000e-135 492.0
5 TraesCS1D01G259400 chr1B 93.885 278 10 5 361 637 474452318 474452047 2.810000e-111 412.0
6 TraesCS1D01G259400 chr1B 95.918 245 8 2 3473 3715 474449001 474448757 2.830000e-106 396.0
7 TraesCS1D01G259400 chr3B 76.655 574 118 11 1067 1632 672744666 672744101 1.770000e-78 303.0
8 TraesCS1D01G259400 chr3D 78.808 453 81 11 1067 1510 511181109 511180663 1.380000e-74 291.0
9 TraesCS1D01G259400 chr3A 93.158 190 13 0 3724 3913 749459862 749459673 2.980000e-71 279.0
10 TraesCS1D01G259400 chr2A 90.000 70 7 0 3408 3477 38315994 38316063 1.500000e-14 91.6
11 TraesCS1D01G259400 chr5A 94.737 57 3 0 3408 3464 6168114 6168170 5.390000e-14 89.8
12 TraesCS1D01G259400 chr6A 92.683 41 3 0 2533 2573 608491703 608491663 4.220000e-05 60.2


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 TraesCS1D01G259400 chr1D 352232387 352236299 3912 True 7227.00 7227 100.000 1 3913 1 chr1D.!!$R1 3912
1 TraesCS1D01G259400 chr1A 452758732 452762313 3581 True 2427.00 4663 93.366 2 3319 2 chr1A.!!$R1 3317
2 TraesCS1D01G259400 chr1B 474448757 474452724 3967 True 1340.75 4063 93.861 4 3715 4 chr1B.!!$R1 3711
3 TraesCS1D01G259400 chr3B 672744101 672744666 565 True 303.00 303 76.655 1067 1632 1 chr3B.!!$R1 565

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
566 842 0.104120 AAAAGCCCGCTGGTTGTTTC 59.896 50.0 0.0 0.0 34.21 2.78 F
568 844 0.109723 AAGCCCGCTGGTTGTTTCTA 59.890 50.0 0.0 0.0 32.28 2.10 F
569 845 0.328258 AGCCCGCTGGTTGTTTCTAT 59.672 50.0 0.0 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2777 0.036388 ACTCTGGTGCCACATAACCG 60.036 55.000 0.0 0.0 39.47 4.44 R
2507 2798 4.767255 GCCACCAGAGTGCTCCCG 62.767 72.222 0.0 0.0 43.09 5.14 R
3006 3297 1.351153 GCTACTCCACTTGAAGCGTC 58.649 55.000 0.0 0.0 0.00 5.19 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
24 29 3.742248 CTCCGGTCCTCCCTCCTCC 62.742 73.684 0.00 0.00 0.00 4.30
94 99 2.675242 CCCGGTTCCCACCTATGCA 61.675 63.158 0.00 0.00 41.64 3.96
124 129 3.053455 GAGCTTCAGGTAATCGATTCGG 58.947 50.000 15.25 2.20 0.00 4.30
140 145 3.304251 GGCCTCGCCTCTTCTCTT 58.696 61.111 0.00 0.00 46.69 2.85
142 147 1.044611 GGCCTCGCCTCTTCTCTTAT 58.955 55.000 0.00 0.00 46.69 1.73
143 148 1.414550 GGCCTCGCCTCTTCTCTTATT 59.585 52.381 0.00 0.00 46.69 1.40
144 149 2.158885 GGCCTCGCCTCTTCTCTTATTT 60.159 50.000 0.00 0.00 46.69 1.40
145 150 3.536570 GCCTCGCCTCTTCTCTTATTTT 58.463 45.455 0.00 0.00 0.00 1.82
146 151 3.942115 GCCTCGCCTCTTCTCTTATTTTT 59.058 43.478 0.00 0.00 0.00 1.94
147 152 4.034626 GCCTCGCCTCTTCTCTTATTTTTC 59.965 45.833 0.00 0.00 0.00 2.29
148 153 5.423886 CCTCGCCTCTTCTCTTATTTTTCT 58.576 41.667 0.00 0.00 0.00 2.52
149 154 5.293079 CCTCGCCTCTTCTCTTATTTTTCTG 59.707 44.000 0.00 0.00 0.00 3.02
168 173 8.477419 TTTTCTGGATTTTGTAGATGTTCCTT 57.523 30.769 0.00 0.00 0.00 3.36
175 180 6.500684 TTTTGTAGATGTTCCTTCATGCTC 57.499 37.500 0.00 0.00 0.00 4.26
195 200 2.176273 GCTGTGGCGCGAATGATCT 61.176 57.895 12.10 0.00 0.00 2.75
198 203 0.726827 TGTGGCGCGAATGATCTTTC 59.273 50.000 12.10 10.56 0.00 2.62
206 211 1.256376 CGAATGATCTTTCGGAGTGCG 59.744 52.381 27.34 0.00 43.59 5.34
359 574 2.282674 CTGGGGAAGCAGCAGCAA 60.283 61.111 3.17 0.00 45.49 3.91
385 660 2.307153 CGGGAGGGAAATCAGGGAA 58.693 57.895 0.00 0.00 0.00 3.97
520 796 3.330275 GCCGTTCGCTTCTGTTGT 58.670 55.556 0.00 0.00 0.00 3.32
536 812 7.010923 GCTTCTGTTGTGAGAAATCGAGATATT 59.989 37.037 0.00 0.00 31.52 1.28
538 814 9.869757 TTCTGTTGTGAGAAATCGAGATATTTA 57.130 29.630 0.00 0.00 0.00 1.40
565 841 0.539518 AAAAAGCCCGCTGGTTGTTT 59.460 45.000 0.00 0.00 34.21 2.83
566 842 0.104120 AAAAGCCCGCTGGTTGTTTC 59.896 50.000 0.00 0.00 34.21 2.78
567 843 0.755327 AAAGCCCGCTGGTTGTTTCT 60.755 50.000 0.00 0.00 34.21 2.52
568 844 0.109723 AAGCCCGCTGGTTGTTTCTA 59.890 50.000 0.00 0.00 32.28 2.10
569 845 0.328258 AGCCCGCTGGTTGTTTCTAT 59.672 50.000 0.00 0.00 0.00 1.98
648 924 5.356426 GGTTGCAAGTTTCCACTTATGTTT 58.644 37.500 0.00 0.00 41.69 2.83
650 926 6.419710 GGTTGCAAGTTTCCACTTATGTTTAC 59.580 38.462 0.00 0.00 41.69 2.01
652 928 6.734137 TGCAAGTTTCCACTTATGTTTACAG 58.266 36.000 0.00 0.00 41.69 2.74
654 930 6.856426 GCAAGTTTCCACTTATGTTTACAGAC 59.144 38.462 0.00 0.00 41.69 3.51
656 932 8.402472 CAAGTTTCCACTTATGTTTACAGACAA 58.598 33.333 0.00 0.00 41.69 3.18
657 933 8.154649 AGTTTCCACTTATGTTTACAGACAAG 57.845 34.615 0.00 0.00 32.47 3.16
732 1019 2.163412 TGCGACCAATTGCACTTATTCC 59.837 45.455 0.00 0.00 40.54 3.01
735 1022 4.662145 CGACCAATTGCACTTATTCCTTC 58.338 43.478 0.00 0.00 0.00 3.46
837 1124 6.017440 TGTCCTTGTGTTATGCTTTTCAGTAC 60.017 38.462 0.00 0.00 0.00 2.73
890 1177 2.338577 ATGGCTGCTATCACCAACTC 57.661 50.000 0.00 0.00 36.94 3.01
898 1186 4.758688 TGCTATCACCAACTCTATGTGTG 58.241 43.478 0.00 0.00 0.00 3.82
948 1236 2.480845 ACGTGTAGGTGAAGCTTGAAC 58.519 47.619 2.10 0.00 0.00 3.18
971 1259 3.040147 ACAAGTGGTATTGTCACGGAG 57.960 47.619 0.00 0.00 39.13 4.63
978 1266 1.112113 TATTGTCACGGAGGAGAGGC 58.888 55.000 0.00 0.00 0.00 4.70
979 1267 1.617947 ATTGTCACGGAGGAGAGGCC 61.618 60.000 0.00 0.00 0.00 5.19
1036 1324 3.198635 TGCTCCTCTGAGGGTTATTCTTG 59.801 47.826 23.00 4.58 39.14 3.02
1042 1330 5.086104 TCTGAGGGTTATTCTTGTACTGC 57.914 43.478 0.00 0.00 0.00 4.40
1054 1342 3.133901 TCTTGTACTGCTGTTGGTCTTCA 59.866 43.478 0.09 0.00 0.00 3.02
1265 1556 2.305927 GTCTCCAGGGTTCATTTCCTCA 59.694 50.000 0.00 0.00 0.00 3.86
1281 1572 3.614092 TCCTCATGGTCTTCAGAATTGC 58.386 45.455 0.00 0.00 34.23 3.56
1616 1907 1.308877 AATCAAGGGCTATGTGGGGT 58.691 50.000 0.00 0.00 0.00 4.95
1635 1926 3.960102 GGGTTCCATTAGATGAATGCCAA 59.040 43.478 0.00 0.00 43.25 4.52
1665 1956 3.595108 GAGCAAGAACAACGCGGCC 62.595 63.158 12.47 0.00 0.00 6.13
1725 2016 9.709495 ATCATAATTGTTGCAATAGTTGTGTTT 57.291 25.926 20.73 11.56 0.00 2.83
1952 2243 7.444629 TGAGAATCCAGTTTCAAAGATGAAG 57.555 36.000 0.00 0.00 45.82 3.02
2066 2357 4.038402 CCTGATGGTTCTTTTCTTGCTGTT 59.962 41.667 0.00 0.00 0.00 3.16
2252 2543 3.170717 TCAGTTACACGAAGAGGGGAAT 58.829 45.455 0.00 0.00 0.00 3.01
2258 2549 2.305927 ACACGAAGAGGGGAATGATTGT 59.694 45.455 0.00 0.00 0.00 2.71
2375 2666 5.224888 CGCAATATAAGCTCCAAATGCATT 58.775 37.500 5.99 5.99 33.00 3.56
2468 2759 3.087031 CCATCTCAGCACCTTTGTCAAT 58.913 45.455 0.00 0.00 0.00 2.57
2486 2777 6.070656 TGTCAATGGGGAATTTGGAGATATC 58.929 40.000 0.00 0.00 0.00 1.63
2507 2798 2.629051 GGTTATGTGGCACCAGAGTAC 58.371 52.381 16.26 4.70 32.74 2.73
2516 2807 1.076906 ACCAGAGTACGGGAGCACT 59.923 57.895 8.05 0.00 39.70 4.40
3006 3297 9.897744 AATATTTTGTCCATGAGCATTATTACG 57.102 29.630 0.00 0.00 0.00 3.18
3008 3299 5.984233 TTGTCCATGAGCATTATTACGAC 57.016 39.130 0.00 0.00 0.00 4.34
3159 3450 6.963083 ATGGAGTACCTGTTAGTTAGCTAG 57.037 41.667 0.00 0.00 37.04 3.42
3173 3464 6.202516 AGTTAGCTAGCTCTTGAGTTACTG 57.797 41.667 23.26 0.00 0.00 2.74
3201 3493 1.290009 GCCATATTGGGATTGCGCC 59.710 57.895 4.18 0.00 38.19 6.53
3241 3533 0.612732 CTGGCCTTCTGGATTTGGCA 60.613 55.000 3.32 0.00 46.53 4.92
3259 3551 4.643387 AAGGCGGCGCTTTCCTGT 62.643 61.111 32.30 5.41 0.00 4.00
3260 3552 4.643387 AGGCGGCGCTTTCCTGTT 62.643 61.111 32.30 4.48 0.00 3.16
3272 3564 1.757682 TTCCTGTTGGCGTTGTCTTT 58.242 45.000 0.00 0.00 0.00 2.52
3275 3567 1.608590 CCTGTTGGCGTTGTCTTTGAT 59.391 47.619 0.00 0.00 0.00 2.57
3321 3613 2.093869 GCATGTGTTGCCAAGGATGATT 60.094 45.455 0.00 0.00 46.15 2.57
3339 3631 4.165036 TGATTGTTAATGTTGATGCGTGC 58.835 39.130 0.00 0.00 0.00 5.34
3364 3656 2.031157 GTGCACTTGGGTGTCATGTTAC 60.031 50.000 10.32 0.00 44.65 2.50
3365 3657 2.226330 GCACTTGGGTGTCATGTTACA 58.774 47.619 0.00 0.00 44.65 2.41
3366 3658 2.621055 GCACTTGGGTGTCATGTTACAA 59.379 45.455 0.00 0.00 44.65 2.41
3367 3659 3.255642 GCACTTGGGTGTCATGTTACAAT 59.744 43.478 0.00 0.00 44.65 2.71
3368 3660 4.797471 CACTTGGGTGTCATGTTACAATG 58.203 43.478 0.00 0.00 38.54 2.82
3371 3663 5.009610 ACTTGGGTGTCATGTTACAATGTTC 59.990 40.000 0.00 0.00 30.70 3.18
3372 3664 4.724399 TGGGTGTCATGTTACAATGTTCT 58.276 39.130 0.00 0.00 0.00 3.01
3373 3665 4.759693 TGGGTGTCATGTTACAATGTTCTC 59.240 41.667 0.00 0.00 0.00 2.87
3391 3757 8.924511 ATGTTCTCTTGTCCTTTATTGAGAAA 57.075 30.769 0.00 0.00 40.64 2.52
3428 3794 4.377431 GCGAATGTCTGAAACTGTACCTTG 60.377 45.833 0.00 0.00 0.00 3.61
3440 3806 3.674278 ACCTTGTGGTGCTCCCTT 58.326 55.556 1.59 0.00 46.51 3.95
3443 3809 1.071471 CTTGTGGTGCTCCCTTCGT 59.929 57.895 1.59 0.00 0.00 3.85
3452 3818 2.616842 GTGCTCCCTTCGTTCAGAAAAA 59.383 45.455 0.00 0.00 38.57 1.94
3465 3831 3.399330 TCAGAAAAATGGACGTCTGACC 58.601 45.455 16.46 0.00 41.13 4.02
3470 3836 1.153568 ATGGACGTCTGACCATGCG 60.154 57.895 16.46 0.00 46.68 4.73
3471 3837 1.888436 ATGGACGTCTGACCATGCGT 61.888 55.000 16.46 0.00 46.68 5.24
3472 3838 2.094659 GGACGTCTGACCATGCGTG 61.095 63.158 16.46 0.00 37.71 5.34
3475 3841 2.863153 GTCTGACCATGCGTGCAC 59.137 61.111 6.82 6.82 0.00 4.57
3476 3842 1.669115 GTCTGACCATGCGTGCACT 60.669 57.895 16.19 0.00 0.00 4.40
3477 3843 1.668793 TCTGACCATGCGTGCACTG 60.669 57.895 16.19 9.73 0.00 3.66
3478 3844 1.668793 CTGACCATGCGTGCACTGA 60.669 57.895 16.19 0.62 0.00 3.41
3480 3846 1.020861 TGACCATGCGTGCACTGATC 61.021 55.000 16.19 3.45 0.00 2.92
3481 3847 1.709147 GACCATGCGTGCACTGATCC 61.709 60.000 16.19 0.00 0.00 3.36
3482 3848 1.746239 CCATGCGTGCACTGATCCA 60.746 57.895 16.19 4.50 0.00 3.41
3483 3849 1.307355 CCATGCGTGCACTGATCCAA 61.307 55.000 16.19 0.00 0.00 3.53
3485 3851 0.806868 ATGCGTGCACTGATCCAAAG 59.193 50.000 16.19 0.00 0.00 2.77
3510 4059 1.002250 GACGTAGGTGTCGTGTGCTG 61.002 60.000 0.00 0.00 41.64 4.41
3519 4068 1.597195 TGTCGTGTGCTGAAACATGTC 59.403 47.619 0.00 0.00 38.10 3.06
3570 4119 7.056006 TCCTGATGATAAATTACATGTGCTGT 58.944 34.615 9.11 0.00 42.13 4.40
3594 4143 2.096218 GCGTTGTGGACTGAAATCTGAC 60.096 50.000 0.00 0.00 0.00 3.51
3715 4264 3.304458 CCCGGCTAAAAACAGAAAGTGTC 60.304 47.826 0.00 0.00 39.03 3.67
3716 4265 3.314080 CCGGCTAAAAACAGAAAGTGTCA 59.686 43.478 0.00 0.00 39.03 3.58
3717 4266 4.201970 CCGGCTAAAAACAGAAAGTGTCAA 60.202 41.667 0.00 0.00 39.03 3.18
3718 4267 4.733405 CGGCTAAAAACAGAAAGTGTCAAC 59.267 41.667 0.00 0.00 39.03 3.18
3719 4268 5.041287 GGCTAAAAACAGAAAGTGTCAACC 58.959 41.667 0.00 0.00 39.03 3.77
3720 4269 5.163550 GGCTAAAAACAGAAAGTGTCAACCT 60.164 40.000 0.00 0.00 39.03 3.50
3721 4270 5.743872 GCTAAAAACAGAAAGTGTCAACCTG 59.256 40.000 0.00 0.00 39.03 4.00
3722 4271 5.975693 AAAAACAGAAAGTGTCAACCTGA 57.024 34.783 0.00 0.00 39.03 3.86
3731 4280 3.212450 GTCAACCTGACGGAAGGAC 57.788 57.895 12.20 0.00 40.02 3.85
3732 4281 0.320508 GTCAACCTGACGGAAGGACC 60.321 60.000 12.20 0.00 40.02 4.46
3733 4282 0.471211 TCAACCTGACGGAAGGACCT 60.471 55.000 12.20 0.00 40.02 3.85
3734 4283 0.320771 CAACCTGACGGAAGGACCTG 60.321 60.000 12.20 3.52 40.02 4.00
3735 4284 2.113243 AACCTGACGGAAGGACCTGC 62.113 60.000 12.20 0.00 40.02 4.85
3736 4285 2.125912 CTGACGGAAGGACCTGCG 60.126 66.667 0.00 0.00 36.31 5.18
3737 4286 3.649277 CTGACGGAAGGACCTGCGG 62.649 68.421 5.47 5.47 34.00 5.69
3738 4287 4.452733 GACGGAAGGACCTGCGGG 62.453 72.222 11.02 11.02 34.00 6.13
3741 4290 4.115199 GGAAGGACCTGCGGGCAT 62.115 66.667 12.89 0.00 35.63 4.40
3742 4291 2.825836 GAAGGACCTGCGGGCATG 60.826 66.667 12.89 0.00 35.63 4.06
3746 4295 4.783621 GACCTGCGGGCATGCTCA 62.784 66.667 19.64 12.38 35.63 4.26
3747 4296 4.119363 ACCTGCGGGCATGCTCAT 62.119 61.111 19.64 0.00 35.63 2.90
3748 4297 2.831742 CCTGCGGGCATGCTCATT 60.832 61.111 19.64 0.00 35.36 2.57
3749 4298 2.411701 CTGCGGGCATGCTCATTG 59.588 61.111 19.64 1.95 35.36 2.82
3750 4299 2.045143 TGCGGGCATGCTCATTGA 60.045 55.556 19.64 0.00 35.36 2.57
3751 4300 1.452953 CTGCGGGCATGCTCATTGAT 61.453 55.000 19.64 0.00 35.36 2.57
3752 4301 1.285023 GCGGGCATGCTCATTGATC 59.715 57.895 19.64 0.00 0.00 2.92
3753 4302 1.954528 CGGGCATGCTCATTGATCC 59.045 57.895 19.64 6.83 0.00 3.36
3754 4303 0.536687 CGGGCATGCTCATTGATCCT 60.537 55.000 19.64 0.00 0.00 3.24
3755 4304 1.245732 GGGCATGCTCATTGATCCTC 58.754 55.000 18.92 0.00 0.00 3.71
3756 4305 0.873054 GGCATGCTCATTGATCCTCG 59.127 55.000 18.92 0.00 0.00 4.63
3757 4306 1.541889 GGCATGCTCATTGATCCTCGA 60.542 52.381 18.92 0.00 0.00 4.04
3758 4307 2.424557 GCATGCTCATTGATCCTCGAT 58.575 47.619 11.37 0.00 0.00 3.59
3759 4308 3.593096 GCATGCTCATTGATCCTCGATA 58.407 45.455 11.37 0.00 0.00 2.92
3760 4309 4.190001 GCATGCTCATTGATCCTCGATAT 58.810 43.478 11.37 0.00 0.00 1.63
3761 4310 4.634883 GCATGCTCATTGATCCTCGATATT 59.365 41.667 11.37 0.00 0.00 1.28
3762 4311 5.123502 GCATGCTCATTGATCCTCGATATTT 59.876 40.000 11.37 0.00 0.00 1.40
3763 4312 6.349115 GCATGCTCATTGATCCTCGATATTTT 60.349 38.462 11.37 0.00 0.00 1.82
3764 4313 7.591165 CATGCTCATTGATCCTCGATATTTTT 58.409 34.615 0.00 0.00 0.00 1.94
3765 4314 6.962686 TGCTCATTGATCCTCGATATTTTTG 58.037 36.000 0.00 0.00 0.00 2.44
3766 4315 5.855395 GCTCATTGATCCTCGATATTTTTGC 59.145 40.000 0.00 0.00 0.00 3.68
3767 4316 6.293845 GCTCATTGATCCTCGATATTTTTGCT 60.294 38.462 0.00 0.00 0.00 3.91
3768 4317 6.962686 TCATTGATCCTCGATATTTTTGCTG 58.037 36.000 0.00 0.00 0.00 4.41
3769 4318 4.818534 TGATCCTCGATATTTTTGCTGC 57.181 40.909 0.00 0.00 0.00 5.25
3770 4319 4.454678 TGATCCTCGATATTTTTGCTGCT 58.545 39.130 0.00 0.00 0.00 4.24
3771 4320 4.274214 TGATCCTCGATATTTTTGCTGCTG 59.726 41.667 0.00 0.00 0.00 4.41
3772 4321 2.355756 TCCTCGATATTTTTGCTGCTGC 59.644 45.455 8.89 8.89 40.20 5.25
3773 4322 2.542411 CCTCGATATTTTTGCTGCTGCC 60.542 50.000 13.47 0.00 38.71 4.85
3774 4323 2.357009 CTCGATATTTTTGCTGCTGCCT 59.643 45.455 13.47 0.00 38.71 4.75
3775 4324 2.355756 TCGATATTTTTGCTGCTGCCTC 59.644 45.455 13.47 0.00 38.71 4.70
3776 4325 2.724349 GATATTTTTGCTGCTGCCTCG 58.276 47.619 13.47 0.00 38.71 4.63
3777 4326 0.810648 TATTTTTGCTGCTGCCTCGG 59.189 50.000 13.47 0.00 38.71 4.63
3778 4327 1.880819 ATTTTTGCTGCTGCCTCGGG 61.881 55.000 13.47 0.00 38.71 5.14
3779 4328 3.790416 TTTTGCTGCTGCCTCGGGT 62.790 57.895 13.47 0.00 38.71 5.28
3780 4329 4.704833 TTGCTGCTGCCTCGGGTC 62.705 66.667 13.47 0.00 38.71 4.46
3782 4331 4.400961 GCTGCTGCCTCGGGTCTT 62.401 66.667 3.85 0.00 0.00 3.01
3783 4332 2.125350 CTGCTGCCTCGGGTCTTC 60.125 66.667 0.00 0.00 0.00 2.87
3784 4333 3.997064 CTGCTGCCTCGGGTCTTCG 62.997 68.421 0.00 0.00 0.00 3.79
3792 4341 3.110178 CGGGTCTTCGCGTCAACC 61.110 66.667 5.77 11.82 43.36 3.77
3793 4342 2.342648 GGGTCTTCGCGTCAACCT 59.657 61.111 20.11 0.00 32.22 3.50
3794 4343 2.027625 GGGTCTTCGCGTCAACCTG 61.028 63.158 20.11 1.46 32.22 4.00
3795 4344 1.006571 GGTCTTCGCGTCAACCTGA 60.007 57.895 5.77 0.00 0.00 3.86
3796 4345 1.282930 GGTCTTCGCGTCAACCTGAC 61.283 60.000 5.77 5.30 43.65 3.51
3805 4354 1.372997 TCAACCTGACGAAGAGCGC 60.373 57.895 0.00 0.00 46.04 5.92
3806 4355 2.430921 AACCTGACGAAGAGCGCG 60.431 61.111 0.00 0.00 46.04 6.86
3807 4356 3.916392 AACCTGACGAAGAGCGCGG 62.916 63.158 8.83 0.00 46.04 6.46
3823 4372 3.344215 GGCGCTGCCGATCAGATG 61.344 66.667 7.64 2.15 45.72 2.90
3824 4373 4.010414 GCGCTGCCGATCAGATGC 62.010 66.667 0.00 7.43 45.72 3.91
3825 4374 2.279985 CGCTGCCGATCAGATGCT 60.280 61.111 8.52 0.00 45.72 3.79
3826 4375 2.308769 CGCTGCCGATCAGATGCTC 61.309 63.158 8.52 0.00 45.72 4.26
3827 4376 2.308769 GCTGCCGATCAGATGCTCG 61.309 63.158 8.52 0.00 45.72 5.03
3828 4377 2.279717 TGCCGATCAGATGCTCGC 60.280 61.111 0.72 0.00 32.91 5.03
3829 4378 2.279717 GCCGATCAGATGCTCGCA 60.280 61.111 0.72 0.00 32.91 5.10
3830 4379 1.884464 GCCGATCAGATGCTCGCAA 60.884 57.895 0.00 0.00 32.91 4.85
3831 4380 1.829349 GCCGATCAGATGCTCGCAAG 61.829 60.000 0.00 0.00 32.91 4.01
3840 4389 3.407657 GCTCGCAAGCTCAGATGG 58.592 61.111 0.00 0.00 45.55 3.51
3841 4390 1.153489 GCTCGCAAGCTCAGATGGA 60.153 57.895 0.00 0.00 45.55 3.41
3842 4391 0.532417 GCTCGCAAGCTCAGATGGAT 60.532 55.000 0.00 0.00 45.55 3.41
3843 4392 1.269988 GCTCGCAAGCTCAGATGGATA 60.270 52.381 0.00 0.00 45.55 2.59
3844 4393 2.612471 GCTCGCAAGCTCAGATGGATAT 60.612 50.000 0.00 0.00 45.55 1.63
3845 4394 2.994578 CTCGCAAGCTCAGATGGATATG 59.005 50.000 0.00 0.00 37.18 1.78
3846 4395 2.074576 CGCAAGCTCAGATGGATATGG 58.925 52.381 0.00 0.00 0.00 2.74
3847 4396 2.549563 CGCAAGCTCAGATGGATATGGT 60.550 50.000 0.00 0.00 0.00 3.55
3848 4397 3.072944 GCAAGCTCAGATGGATATGGTC 58.927 50.000 0.00 0.00 0.00 4.02
3849 4398 3.495629 GCAAGCTCAGATGGATATGGTCA 60.496 47.826 0.00 0.00 0.00 4.02
3850 4399 4.063689 CAAGCTCAGATGGATATGGTCAC 58.936 47.826 0.00 0.00 0.00 3.67
3851 4400 3.585360 AGCTCAGATGGATATGGTCACT 58.415 45.455 0.00 0.00 0.00 3.41
3852 4401 4.745351 AGCTCAGATGGATATGGTCACTA 58.255 43.478 0.00 0.00 0.00 2.74
3853 4402 5.150715 AGCTCAGATGGATATGGTCACTAA 58.849 41.667 0.00 0.00 0.00 2.24
3854 4403 5.011533 AGCTCAGATGGATATGGTCACTAAC 59.988 44.000 0.00 0.00 0.00 2.34
3855 4404 5.221521 GCTCAGATGGATATGGTCACTAACA 60.222 44.000 0.00 0.00 0.00 2.41
3856 4405 6.519721 GCTCAGATGGATATGGTCACTAACAT 60.520 42.308 0.00 0.00 0.00 2.71
3857 4406 6.997655 TCAGATGGATATGGTCACTAACATC 58.002 40.000 0.00 0.00 35.07 3.06
3858 4407 6.014242 TCAGATGGATATGGTCACTAACATCC 60.014 42.308 0.00 0.00 35.34 3.51
3859 4408 6.013898 CAGATGGATATGGTCACTAACATCCT 60.014 42.308 6.69 0.00 35.34 3.24
3860 4409 6.560304 AGATGGATATGGTCACTAACATCCTT 59.440 38.462 6.69 1.53 35.34 3.36
3861 4410 6.174720 TGGATATGGTCACTAACATCCTTC 57.825 41.667 6.69 0.00 34.34 3.46
3862 4411 5.221441 TGGATATGGTCACTAACATCCTTCG 60.221 44.000 6.69 0.00 34.34 3.79
3863 4412 2.380084 TGGTCACTAACATCCTTCGC 57.620 50.000 0.00 0.00 0.00 4.70
3864 4413 1.899814 TGGTCACTAACATCCTTCGCT 59.100 47.619 0.00 0.00 0.00 4.93
3865 4414 2.271800 GGTCACTAACATCCTTCGCTG 58.728 52.381 0.00 0.00 0.00 5.18
3866 4415 1.661112 GTCACTAACATCCTTCGCTGC 59.339 52.381 0.00 0.00 0.00 5.25
3867 4416 1.550524 TCACTAACATCCTTCGCTGCT 59.449 47.619 0.00 0.00 0.00 4.24
3868 4417 1.929836 CACTAACATCCTTCGCTGCTC 59.070 52.381 0.00 0.00 0.00 4.26
3869 4418 1.134670 ACTAACATCCTTCGCTGCTCC 60.135 52.381 0.00 0.00 0.00 4.70
3870 4419 0.901827 TAACATCCTTCGCTGCTCCA 59.098 50.000 0.00 0.00 0.00 3.86
3871 4420 0.254178 AACATCCTTCGCTGCTCCAT 59.746 50.000 0.00 0.00 0.00 3.41
3872 4421 0.254178 ACATCCTTCGCTGCTCCATT 59.746 50.000 0.00 0.00 0.00 3.16
3873 4422 0.661552 CATCCTTCGCTGCTCCATTG 59.338 55.000 0.00 0.00 0.00 2.82
3874 4423 0.465097 ATCCTTCGCTGCTCCATTGG 60.465 55.000 0.00 0.00 0.00 3.16
3875 4424 2.117156 CCTTCGCTGCTCCATTGGG 61.117 63.158 2.09 0.00 0.00 4.12
3876 4425 2.751436 TTCGCTGCTCCATTGGGC 60.751 61.111 2.09 6.06 0.00 5.36
3880 4429 2.361610 CTGCTCCATTGGGCGGTT 60.362 61.111 13.79 0.00 0.00 4.44
3881 4430 2.361104 TGCTCCATTGGGCGGTTC 60.361 61.111 2.09 0.00 0.00 3.62
3882 4431 3.140814 GCTCCATTGGGCGGTTCC 61.141 66.667 2.09 0.00 0.00 3.62
3898 4447 4.522722 GGTTCCCGATCAAGTATCTAGG 57.477 50.000 0.00 0.00 31.87 3.02
3899 4448 3.306156 GGTTCCCGATCAAGTATCTAGGC 60.306 52.174 0.00 0.00 31.87 3.93
3900 4449 2.526432 TCCCGATCAAGTATCTAGGCC 58.474 52.381 0.00 0.00 31.87 5.19
3901 4450 2.110188 TCCCGATCAAGTATCTAGGCCT 59.890 50.000 11.78 11.78 31.87 5.19
3902 4451 2.494073 CCCGATCAAGTATCTAGGCCTC 59.506 54.545 9.68 0.00 31.87 4.70
3903 4452 2.494073 CCGATCAAGTATCTAGGCCTCC 59.506 54.545 9.68 0.00 31.87 4.30
3904 4453 2.494073 CGATCAAGTATCTAGGCCTCCC 59.506 54.545 9.68 0.00 31.87 4.30
3905 4454 1.996798 TCAAGTATCTAGGCCTCCCG 58.003 55.000 9.68 0.00 35.76 5.14
3906 4455 1.217183 TCAAGTATCTAGGCCTCCCGT 59.783 52.381 9.68 0.00 35.76 5.28
3907 4456 2.040178 CAAGTATCTAGGCCTCCCGTT 58.960 52.381 9.68 0.00 35.76 4.44
3908 4457 1.705873 AGTATCTAGGCCTCCCGTTG 58.294 55.000 9.68 0.00 35.76 4.10
3909 4458 1.217183 AGTATCTAGGCCTCCCGTTGA 59.783 52.381 9.68 0.00 35.76 3.18
3910 4459 1.340568 GTATCTAGGCCTCCCGTTGAC 59.659 57.143 9.68 0.00 35.76 3.18
3911 4460 1.049289 ATCTAGGCCTCCCGTTGACC 61.049 60.000 9.68 0.00 35.76 4.02
3912 4461 1.987855 CTAGGCCTCCCGTTGACCA 60.988 63.158 9.68 0.00 35.76 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 29 1.187087 GAGTCTGTGAGTAGTGGGGG 58.813 60.000 0.00 0.00 0.00 5.40
94 99 4.421479 CTGAAGCTCGCCGTCCGT 62.421 66.667 0.00 0.00 38.35 4.69
124 129 2.900716 AATAAGAGAAGAGGCGAGGC 57.099 50.000 0.00 0.00 0.00 4.70
142 147 8.477419 AGGAACATCTACAAAATCCAGAAAAA 57.523 30.769 0.00 0.00 0.00 1.94
143 148 8.477419 AAGGAACATCTACAAAATCCAGAAAA 57.523 30.769 0.00 0.00 0.00 2.29
144 149 7.723616 TGAAGGAACATCTACAAAATCCAGAAA 59.276 33.333 0.00 0.00 0.00 2.52
145 150 7.230747 TGAAGGAACATCTACAAAATCCAGAA 58.769 34.615 0.00 0.00 0.00 3.02
146 151 6.778821 TGAAGGAACATCTACAAAATCCAGA 58.221 36.000 0.00 0.00 0.00 3.86
147 152 7.478322 CATGAAGGAACATCTACAAAATCCAG 58.522 38.462 0.00 0.00 0.00 3.86
148 153 6.127647 GCATGAAGGAACATCTACAAAATCCA 60.128 38.462 0.00 0.00 0.00 3.41
149 154 6.096001 AGCATGAAGGAACATCTACAAAATCC 59.904 38.462 0.00 0.00 0.00 3.01
159 164 2.355132 CAGCAGAGCATGAAGGAACATC 59.645 50.000 0.00 0.00 0.00 3.06
166 171 1.801332 GCCACAGCAGAGCATGAAG 59.199 57.895 0.00 0.00 39.53 3.02
168 173 2.435410 CGCCACAGCAGAGCATGA 60.435 61.111 0.00 0.00 39.83 3.07
175 180 2.370824 GATCATTCGCGCCACAGCAG 62.371 60.000 0.00 0.00 39.83 4.24
195 200 4.357947 AGCTCGCGCACTCCGAAA 62.358 61.111 8.75 0.00 40.02 3.46
206 211 2.032681 AACCAACCCAGAGCTCGC 59.967 61.111 8.37 0.00 0.00 5.03
232 237 1.303236 CCAAGAACCCGCATCCACA 60.303 57.895 0.00 0.00 0.00 4.17
536 812 5.889289 ACCAGCGGGCTTTTTCTTATTATAA 59.111 36.000 1.46 0.00 37.90 0.98
538 814 4.278310 ACCAGCGGGCTTTTTCTTATTAT 58.722 39.130 1.46 0.00 37.90 1.28
551 827 0.733150 GATAGAAACAACCAGCGGGC 59.267 55.000 1.46 0.00 37.90 6.13
553 829 7.730364 ATTTATAGATAGAAACAACCAGCGG 57.270 36.000 0.00 0.00 0.00 5.52
583 859 2.680312 ACCATCAATCGAGACCACAG 57.320 50.000 0.00 0.00 0.00 3.66
648 924 7.506114 ACTTGTTCTTCCATTACTTGTCTGTA 58.494 34.615 0.00 0.00 0.00 2.74
650 926 6.867662 ACTTGTTCTTCCATTACTTGTCTG 57.132 37.500 0.00 0.00 0.00 3.51
652 928 8.926715 AAAAACTTGTTCTTCCATTACTTGTC 57.073 30.769 0.00 0.00 0.00 3.18
656 932 9.185680 ACAGTAAAAACTTGTTCTTCCATTACT 57.814 29.630 0.00 0.00 32.85 2.24
657 933 9.797556 AACAGTAAAAACTTGTTCTTCCATTAC 57.202 29.630 0.00 0.00 0.00 1.89
758 1045 6.038356 GCCATAGCAAATAACATATGATGCC 58.962 40.000 10.38 0.00 39.53 4.40
805 1092 4.826733 AGCATAACACAAGGACAACATCAA 59.173 37.500 0.00 0.00 0.00 2.57
878 1165 6.096141 AGAGACACACATAGAGTTGGTGATAG 59.904 42.308 0.00 0.00 36.42 2.08
923 1211 2.669364 AGCTTCACCTACACGTAAACG 58.331 47.619 0.04 0.04 46.33 3.60
948 1236 3.056393 TCCGTGACAATACCACTTGTAGG 60.056 47.826 0.00 0.00 39.40 3.18
971 1259 2.187163 GCCTAACGTGGCCTCTCC 59.813 66.667 3.32 0.00 46.82 3.71
978 1266 2.860293 CACTTGCGCCTAACGTGG 59.140 61.111 4.18 0.00 46.11 4.94
979 1267 2.173382 GCACTTGCGCCTAACGTG 59.827 61.111 4.18 6.11 46.11 4.49
1036 1324 3.113260 AGTGAAGACCAACAGCAGTAC 57.887 47.619 0.00 0.00 0.00 2.73
1042 1330 3.788797 GCGAAACAAGTGAAGACCAACAG 60.789 47.826 0.00 0.00 0.00 3.16
1054 1342 1.202698 AGCTTCAGAGGCGAAACAAGT 60.203 47.619 0.00 0.00 34.52 3.16
1265 1556 2.753452 CTGCTGCAATTCTGAAGACCAT 59.247 45.455 3.02 0.00 27.82 3.55
1281 1572 0.463295 CCAGCCCAGTCATACTGCTG 60.463 60.000 10.75 10.75 44.63 4.41
1616 1907 4.539726 AGCTTGGCATTCATCTAATGGAA 58.460 39.130 0.00 0.00 44.45 3.53
1635 1926 2.267174 TCTTGCTCTTTGCTGAAGCT 57.733 45.000 3.61 0.00 43.37 3.74
1665 1956 2.223340 GCCAACAATAGCTCCAACGATG 60.223 50.000 0.00 0.00 0.00 3.84
1725 2016 3.215151 TGGTAATTTCCGCAGACAAACA 58.785 40.909 0.00 0.00 0.00 2.83
1849 2140 3.070878 ACATTGCCTTTCGACCCAAAATT 59.929 39.130 0.00 0.00 0.00 1.82
1952 2243 4.513318 GTGGCCTTCATAAGATCACTTAGC 59.487 45.833 3.32 0.00 41.12 3.09
2066 2357 7.759489 ATGTTGTGAATCTTGTAGCCTTTTA 57.241 32.000 0.00 0.00 0.00 1.52
2252 2543 4.166725 AGAGGCCAATCCATCTTACAATCA 59.833 41.667 5.01 0.00 37.29 2.57
2258 2549 2.707791 CCTCAGAGGCCAATCCATCTTA 59.292 50.000 5.01 0.00 37.29 2.10
2375 2666 2.981898 TCGTAGTCGTCATCCAAGAGA 58.018 47.619 0.00 0.00 38.33 3.10
2468 2759 3.053077 ACCGATATCTCCAAATTCCCCA 58.947 45.455 0.34 0.00 0.00 4.96
2486 2777 0.036388 ACTCTGGTGCCACATAACCG 60.036 55.000 0.00 0.00 39.47 4.44
2507 2798 4.767255 GCCACCAGAGTGCTCCCG 62.767 72.222 0.00 0.00 43.09 5.14
3006 3297 1.351153 GCTACTCCACTTGAAGCGTC 58.649 55.000 0.00 0.00 0.00 5.19
3159 3450 6.456181 GCATAATCACACAGTAACTCAAGAGC 60.456 42.308 0.00 0.00 0.00 4.09
3173 3464 6.392354 CAATCCCAATATGGCATAATCACAC 58.608 40.000 11.86 0.00 35.79 3.82
3241 3533 3.365265 CAGGAAAGCGCCGCCTTT 61.365 61.111 4.98 5.80 37.73 3.11
3259 3551 3.794028 CGAAAAATCAAAGACAACGCCAA 59.206 39.130 0.00 0.00 0.00 4.52
3260 3552 3.065510 TCGAAAAATCAAAGACAACGCCA 59.934 39.130 0.00 0.00 0.00 5.69
3321 3613 2.668001 GCTGCACGCATCAACATTAACA 60.668 45.455 0.00 0.00 38.92 2.41
3347 3639 4.469657 ACATTGTAACATGACACCCAAGT 58.530 39.130 0.00 0.00 0.00 3.16
3352 3644 6.017109 ACAAGAGAACATTGTAACATGACACC 60.017 38.462 0.00 0.00 39.06 4.16
3364 3656 8.327941 TCTCAATAAAGGACAAGAGAACATTG 57.672 34.615 0.00 0.00 0.00 2.82
3365 3657 8.924511 TTCTCAATAAAGGACAAGAGAACATT 57.075 30.769 0.00 0.00 37.24 2.71
3366 3658 8.924511 TTTCTCAATAAAGGACAAGAGAACAT 57.075 30.769 0.00 0.00 40.57 2.71
3367 3659 8.746052 TTTTCTCAATAAAGGACAAGAGAACA 57.254 30.769 0.00 0.00 40.57 3.18
3391 3757 7.970384 TCAGACATTCGCGTCTTATAATTTTT 58.030 30.769 5.77 0.00 43.84 1.94
3396 3762 6.034577 CAGTTTCAGACATTCGCGTCTTATAA 59.965 38.462 5.77 0.00 43.84 0.98
3405 3771 3.326747 AGGTACAGTTTCAGACATTCGC 58.673 45.455 0.00 0.00 0.00 4.70
3428 3794 0.951040 CTGAACGAAGGGAGCACCAC 60.951 60.000 1.58 0.00 43.89 4.16
3440 3806 3.493129 CAGACGTCCATTTTTCTGAACGA 59.507 43.478 13.01 0.00 38.19 3.85
3443 3809 3.813166 GGTCAGACGTCCATTTTTCTGAA 59.187 43.478 13.01 0.00 44.62 3.02
3452 3818 1.153568 CGCATGGTCAGACGTCCAT 60.154 57.895 13.01 6.29 44.15 3.41
3465 3831 0.522626 TTTGGATCAGTGCACGCATG 59.477 50.000 12.01 4.56 0.00 4.06
3502 4051 1.866601 TGAGACATGTTTCAGCACACG 59.133 47.619 14.69 0.00 0.00 4.49
3510 4059 5.065704 TGCTCTAGTCTGAGACATGTTTC 57.934 43.478 15.86 9.40 36.23 2.78
3570 4119 3.684305 CAGATTTCAGTCCACAACGCATA 59.316 43.478 0.00 0.00 0.00 3.14
3594 4143 7.655328 TGATTGCAGTAAATAACAAAAGGTTGG 59.345 33.333 0.00 0.00 40.73 3.77
3715 4264 0.320771 CAGGTCCTTCCGTCAGGTTG 60.321 60.000 0.00 0.00 41.99 3.77
3716 4265 2.058675 CAGGTCCTTCCGTCAGGTT 58.941 57.895 0.00 0.00 41.99 3.50
3717 4266 2.584391 GCAGGTCCTTCCGTCAGGT 61.584 63.158 0.00 0.00 41.99 4.00
3718 4267 2.266055 GCAGGTCCTTCCGTCAGG 59.734 66.667 0.00 0.00 41.99 3.86
3719 4268 2.125912 CGCAGGTCCTTCCGTCAG 60.126 66.667 0.00 0.00 41.99 3.51
3732 4281 1.452953 ATCAATGAGCATGCCCGCAG 61.453 55.000 15.66 2.11 0.00 5.18
3733 4282 1.449726 GATCAATGAGCATGCCCGCA 61.450 55.000 15.66 11.08 0.00 5.69
3734 4283 1.285023 GATCAATGAGCATGCCCGC 59.715 57.895 15.66 4.86 0.00 6.13
3735 4284 0.536687 AGGATCAATGAGCATGCCCG 60.537 55.000 15.66 0.00 0.00 6.13
3736 4285 1.245732 GAGGATCAATGAGCATGCCC 58.754 55.000 15.66 2.04 33.17 5.36
3737 4286 0.873054 CGAGGATCAATGAGCATGCC 59.127 55.000 15.66 6.65 33.17 4.40
3738 4287 1.875009 TCGAGGATCAATGAGCATGC 58.125 50.000 10.51 10.51 33.17 4.06
3739 4288 6.738832 AAATATCGAGGATCAATGAGCATG 57.261 37.500 0.00 0.00 33.17 4.06
3740 4289 7.591165 CAAAAATATCGAGGATCAATGAGCAT 58.409 34.615 0.00 0.00 33.17 3.79
3741 4290 6.513884 GCAAAAATATCGAGGATCAATGAGCA 60.514 38.462 0.00 0.00 33.17 4.26
3742 4291 5.855395 GCAAAAATATCGAGGATCAATGAGC 59.145 40.000 0.00 0.00 33.17 4.26
3743 4292 7.076362 CAGCAAAAATATCGAGGATCAATGAG 58.924 38.462 0.00 0.00 33.17 2.90
3744 4293 6.513884 GCAGCAAAAATATCGAGGATCAATGA 60.514 38.462 0.00 0.00 33.17 2.57
3745 4294 5.628193 GCAGCAAAAATATCGAGGATCAATG 59.372 40.000 0.00 0.00 33.17 2.82
3746 4295 5.533903 AGCAGCAAAAATATCGAGGATCAAT 59.466 36.000 0.00 0.00 33.17 2.57
3747 4296 4.883585 AGCAGCAAAAATATCGAGGATCAA 59.116 37.500 0.00 0.00 33.17 2.57
3748 4297 4.274214 CAGCAGCAAAAATATCGAGGATCA 59.726 41.667 0.00 0.00 33.17 2.92
3749 4298 4.781071 CAGCAGCAAAAATATCGAGGATC 58.219 43.478 0.00 0.00 0.00 3.36
3750 4299 3.004106 GCAGCAGCAAAAATATCGAGGAT 59.996 43.478 0.00 0.00 41.58 3.24
3751 4300 2.355756 GCAGCAGCAAAAATATCGAGGA 59.644 45.455 0.00 0.00 41.58 3.71
3752 4301 2.542411 GGCAGCAGCAAAAATATCGAGG 60.542 50.000 2.65 0.00 44.61 4.63
3753 4302 2.357009 AGGCAGCAGCAAAAATATCGAG 59.643 45.455 2.65 0.00 44.61 4.04
3754 4303 2.355756 GAGGCAGCAGCAAAAATATCGA 59.644 45.455 2.65 0.00 44.61 3.59
3755 4304 2.724349 GAGGCAGCAGCAAAAATATCG 58.276 47.619 2.65 0.00 44.61 2.92
3756 4305 2.542411 CCGAGGCAGCAGCAAAAATATC 60.542 50.000 2.65 0.00 44.61 1.63
3757 4306 1.406539 CCGAGGCAGCAGCAAAAATAT 59.593 47.619 2.65 0.00 44.61 1.28
3758 4307 0.810648 CCGAGGCAGCAGCAAAAATA 59.189 50.000 2.65 0.00 44.61 1.40
3759 4308 1.588082 CCGAGGCAGCAGCAAAAAT 59.412 52.632 2.65 0.00 44.61 1.82
3760 4309 2.563798 CCCGAGGCAGCAGCAAAAA 61.564 57.895 2.65 0.00 44.61 1.94
3761 4310 2.985282 CCCGAGGCAGCAGCAAAA 60.985 61.111 2.65 0.00 44.61 2.44
3762 4311 4.269523 ACCCGAGGCAGCAGCAAA 62.270 61.111 2.65 0.00 44.61 3.68
3763 4312 4.704833 GACCCGAGGCAGCAGCAA 62.705 66.667 2.65 0.00 44.61 3.91
3765 4314 4.400961 AAGACCCGAGGCAGCAGC 62.401 66.667 0.00 0.00 41.10 5.25
3766 4315 2.125350 GAAGACCCGAGGCAGCAG 60.125 66.667 0.00 0.00 0.00 4.24
3767 4316 4.069232 CGAAGACCCGAGGCAGCA 62.069 66.667 0.00 0.00 0.00 4.41
3772 4321 3.277211 TTGACGCGAAGACCCGAGG 62.277 63.158 15.93 0.00 33.70 4.63
3773 4322 2.087009 GTTGACGCGAAGACCCGAG 61.087 63.158 15.93 0.00 35.51 4.63
3774 4323 2.049802 GTTGACGCGAAGACCCGA 60.050 61.111 15.93 0.00 0.00 5.14
3775 4324 3.110178 GGTTGACGCGAAGACCCG 61.110 66.667 15.93 0.00 0.00 5.28
3776 4325 2.027625 CAGGTTGACGCGAAGACCC 61.028 63.158 15.93 5.74 32.53 4.46
3777 4326 1.006571 TCAGGTTGACGCGAAGACC 60.007 57.895 15.93 16.91 0.00 3.85
3778 4327 2.142641 GTCAGGTTGACGCGAAGAC 58.857 57.895 15.93 7.58 37.67 3.01
3779 4328 4.647654 GTCAGGTTGACGCGAAGA 57.352 55.556 15.93 0.00 37.67 2.87
3786 4335 1.618640 GCGCTCTTCGTCAGGTTGAC 61.619 60.000 0.00 0.00 43.65 3.18
3787 4336 1.372997 GCGCTCTTCGTCAGGTTGA 60.373 57.895 0.00 0.00 41.07 3.18
3788 4337 2.720758 CGCGCTCTTCGTCAGGTTG 61.721 63.158 5.56 0.00 41.07 3.77
3789 4338 2.430921 CGCGCTCTTCGTCAGGTT 60.431 61.111 5.56 0.00 41.07 3.50
3790 4339 4.421479 CCGCGCTCTTCGTCAGGT 62.421 66.667 5.56 0.00 41.07 4.00
3806 4355 3.344215 CATCTGATCGGCAGCGCC 61.344 66.667 2.29 9.20 46.75 6.53
3807 4356 4.010414 GCATCTGATCGGCAGCGC 62.010 66.667 0.00 0.00 44.52 5.92
3808 4357 2.279985 AGCATCTGATCGGCAGCG 60.280 61.111 10.97 0.00 44.52 5.18
3809 4358 3.640231 GAGCATCTGATCGGCAGC 58.360 61.111 9.29 9.29 44.52 5.25
3824 4373 2.808523 TATCCATCTGAGCTTGCGAG 57.191 50.000 0.00 0.00 0.00 5.03
3825 4374 2.289257 CCATATCCATCTGAGCTTGCGA 60.289 50.000 0.00 0.00 0.00 5.10
3826 4375 2.074576 CCATATCCATCTGAGCTTGCG 58.925 52.381 0.00 0.00 0.00 4.85
3827 4376 3.072944 GACCATATCCATCTGAGCTTGC 58.927 50.000 0.00 0.00 0.00 4.01
3828 4377 4.063689 GTGACCATATCCATCTGAGCTTG 58.936 47.826 0.00 0.00 0.00 4.01
3829 4378 3.972638 AGTGACCATATCCATCTGAGCTT 59.027 43.478 0.00 0.00 0.00 3.74
3830 4379 3.585360 AGTGACCATATCCATCTGAGCT 58.415 45.455 0.00 0.00 0.00 4.09
3831 4380 5.221521 TGTTAGTGACCATATCCATCTGAGC 60.222 44.000 0.00 0.00 0.00 4.26
3832 4381 6.410942 TGTTAGTGACCATATCCATCTGAG 57.589 41.667 0.00 0.00 0.00 3.35
3833 4382 6.014242 GGATGTTAGTGACCATATCCATCTGA 60.014 42.308 0.00 0.00 35.35 3.27
3834 4383 6.013898 AGGATGTTAGTGACCATATCCATCTG 60.014 42.308 9.76 0.00 37.21 2.90
3835 4384 6.087456 AGGATGTTAGTGACCATATCCATCT 58.913 40.000 9.76 0.00 37.21 2.90
3836 4385 6.365970 AGGATGTTAGTGACCATATCCATC 57.634 41.667 9.76 0.00 37.21 3.51
3837 4386 6.519043 CGAAGGATGTTAGTGACCATATCCAT 60.519 42.308 9.76 0.00 37.21 3.41
3838 4387 5.221441 CGAAGGATGTTAGTGACCATATCCA 60.221 44.000 9.76 0.00 37.21 3.41
3839 4388 5.230942 CGAAGGATGTTAGTGACCATATCC 58.769 45.833 0.00 0.00 35.46 2.59
3840 4389 4.686554 GCGAAGGATGTTAGTGACCATATC 59.313 45.833 0.00 0.00 0.00 1.63
3841 4390 4.345257 AGCGAAGGATGTTAGTGACCATAT 59.655 41.667 0.00 0.00 0.00 1.78
3842 4391 3.704566 AGCGAAGGATGTTAGTGACCATA 59.295 43.478 0.00 0.00 0.00 2.74
3843 4392 2.501723 AGCGAAGGATGTTAGTGACCAT 59.498 45.455 0.00 0.00 0.00 3.55
3844 4393 1.899814 AGCGAAGGATGTTAGTGACCA 59.100 47.619 0.00 0.00 0.00 4.02
3845 4394 2.271800 CAGCGAAGGATGTTAGTGACC 58.728 52.381 0.00 0.00 0.00 4.02
3846 4395 1.661112 GCAGCGAAGGATGTTAGTGAC 59.339 52.381 0.00 0.00 0.00 3.67
3847 4396 1.550524 AGCAGCGAAGGATGTTAGTGA 59.449 47.619 0.00 0.00 0.00 3.41
3848 4397 1.929836 GAGCAGCGAAGGATGTTAGTG 59.070 52.381 0.00 0.00 0.00 2.74
3849 4398 1.134670 GGAGCAGCGAAGGATGTTAGT 60.135 52.381 0.00 0.00 0.00 2.24
3850 4399 1.134699 TGGAGCAGCGAAGGATGTTAG 60.135 52.381 0.00 0.00 0.00 2.34
3851 4400 0.901827 TGGAGCAGCGAAGGATGTTA 59.098 50.000 0.00 0.00 0.00 2.41
3852 4401 0.254178 ATGGAGCAGCGAAGGATGTT 59.746 50.000 0.00 0.00 0.00 2.71
3853 4402 0.254178 AATGGAGCAGCGAAGGATGT 59.746 50.000 0.00 0.00 0.00 3.06
3854 4403 0.661552 CAATGGAGCAGCGAAGGATG 59.338 55.000 0.00 0.00 0.00 3.51
3855 4404 0.465097 CCAATGGAGCAGCGAAGGAT 60.465 55.000 0.00 0.00 0.00 3.24
3856 4405 1.078214 CCAATGGAGCAGCGAAGGA 60.078 57.895 0.00 0.00 0.00 3.36
3857 4406 2.117156 CCCAATGGAGCAGCGAAGG 61.117 63.158 0.00 0.00 0.00 3.46
3858 4407 2.768492 GCCCAATGGAGCAGCGAAG 61.768 63.158 0.00 0.00 0.00 3.79
3859 4408 2.751436 GCCCAATGGAGCAGCGAA 60.751 61.111 0.00 0.00 0.00 4.70
3863 4412 2.361610 AACCGCCCAATGGAGCAG 60.362 61.111 0.00 0.00 0.00 4.24
3864 4413 2.361104 GAACCGCCCAATGGAGCA 60.361 61.111 0.00 0.00 0.00 4.26
3865 4414 3.140814 GGAACCGCCCAATGGAGC 61.141 66.667 0.00 1.26 0.00 4.70
3878 4427 3.306156 GGCCTAGATACTTGATCGGGAAC 60.306 52.174 0.00 0.00 39.80 3.62
3879 4428 2.897969 GGCCTAGATACTTGATCGGGAA 59.102 50.000 0.00 0.00 39.80 3.97
3880 4429 2.110188 AGGCCTAGATACTTGATCGGGA 59.890 50.000 1.29 0.00 39.80 5.14
3881 4430 2.494073 GAGGCCTAGATACTTGATCGGG 59.506 54.545 4.42 0.00 39.80 5.14
3882 4431 2.494073 GGAGGCCTAGATACTTGATCGG 59.506 54.545 4.42 0.00 39.80 4.18
3883 4432 2.494073 GGGAGGCCTAGATACTTGATCG 59.506 54.545 4.42 0.00 39.80 3.69
3884 4433 2.494073 CGGGAGGCCTAGATACTTGATC 59.506 54.545 4.42 0.00 34.40 2.92
3885 4434 2.158295 ACGGGAGGCCTAGATACTTGAT 60.158 50.000 4.42 0.00 0.00 2.57
3886 4435 1.217183 ACGGGAGGCCTAGATACTTGA 59.783 52.381 4.42 0.00 0.00 3.02
3887 4436 1.705873 ACGGGAGGCCTAGATACTTG 58.294 55.000 4.42 0.00 0.00 3.16
3888 4437 2.040178 CAACGGGAGGCCTAGATACTT 58.960 52.381 4.42 0.00 0.00 2.24
3889 4438 1.217183 TCAACGGGAGGCCTAGATACT 59.783 52.381 4.42 0.00 0.00 2.12
3890 4439 1.340568 GTCAACGGGAGGCCTAGATAC 59.659 57.143 4.42 0.00 0.00 2.24
3891 4440 1.700955 GTCAACGGGAGGCCTAGATA 58.299 55.000 4.42 0.00 0.00 1.98
3892 4441 1.049289 GGTCAACGGGAGGCCTAGAT 61.049 60.000 4.42 0.00 0.00 1.98
3893 4442 1.684734 GGTCAACGGGAGGCCTAGA 60.685 63.158 4.42 0.00 0.00 2.43
3894 4443 1.987855 TGGTCAACGGGAGGCCTAG 60.988 63.158 4.42 2.40 0.00 3.02
3895 4444 2.120940 TGGTCAACGGGAGGCCTA 59.879 61.111 4.42 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.