Multiple sequence alignment - TraesCS5B01G375900

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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 TraesCS5B01G375900 chr5B 100.000 3788 0 0 1 3788 553724094 553727881 0.000000e+00 6996.0
1 TraesCS5B01G375900 chr5B 87.581 1538 169 19 1232 2755 29337728 29339257 0.000000e+00 1762.0
2 TraesCS5B01G375900 chr5A 91.856 3303 135 66 8 3260 572020540 572023758 0.000000e+00 4486.0
3 TraesCS5B01G375900 chr5A 87.581 1538 168 20 1232 2755 27516306 27517834 0.000000e+00 1760.0
4 TraesCS5B01G375900 chr5A 88.177 203 19 5 3380 3581 572023986 572024184 1.760000e-58 237.0
5 TraesCS5B01G375900 chr5D 93.436 3047 93 29 279 3260 453238037 453241041 0.000000e+00 4420.0
6 TraesCS5B01G375900 chr5D 87.451 1538 171 19 1232 2755 38724108 38725637 0.000000e+00 1751.0
7 TraesCS5B01G375900 chr5D 93.846 130 8 0 3350 3479 453241207 453241336 2.990000e-46 196.0
8 TraesCS5B01G375900 chr5D 91.509 106 6 3 3259 3362 453241085 453241189 3.940000e-30 143.0
9 TraesCS5B01G375900 chr1D 95.556 45 2 0 1318 1362 445097742 445097698 5.250000e-09 73.1
10 TraesCS5B01G375900 chr1B 93.333 45 3 0 1318 1362 606254096 606254052 2.440000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G375900 chr5B 553724094 553727881 3787 False 6996.000000 6996 100.000000 1 3788 1 chr5B.!!$F2 3787
1 TraesCS5B01G375900 chr5B 29337728 29339257 1529 False 1762.000000 1762 87.581000 1232 2755 1 chr5B.!!$F1 1523
2 TraesCS5B01G375900 chr5A 572020540 572024184 3644 False 2361.500000 4486 90.016500 8 3581 2 chr5A.!!$F2 3573
3 TraesCS5B01G375900 chr5A 27516306 27517834 1528 False 1760.000000 1760 87.581000 1232 2755 1 chr5A.!!$F1 1523
4 TraesCS5B01G375900 chr5D 38724108 38725637 1529 False 1751.000000 1751 87.451000 1232 2755 1 chr5D.!!$F1 1523
5 TraesCS5B01G375900 chr5D 453238037 453241336 3299 False 1586.333333 4420 92.930333 279 3479 3 chr5D.!!$F2 3200

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
55 56 0.395036 TTGGGCATACGGATGTTGGG 60.395 55.000 9.9 0.0 35.30 4.12 F
129 130 0.832135 GGTCGAGGCCCTGGATGATA 60.832 60.000 0.0 0.0 0.00 2.15 F
785 826 1.068083 CCACACTCCCATCGATCCG 59.932 63.158 0.0 0.0 0.00 4.18 F
802 843 1.068895 TCCGTCTCTTTTACCAACGCA 59.931 47.619 0.0 0.0 32.26 5.24 F
1797 1868 2.361610 ATCCCGTACCACGTCCGT 60.362 61.111 0.0 0.0 40.58 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1841 1.033746 GGTACGGGATGTCGTCCTCA 61.034 60.000 10.99 0.00 46.91 3.86 R
1905 1976 3.428282 TCGTAGCTGAGCGCGTGA 61.428 61.111 19.71 6.08 45.59 4.35 R
2289 2360 1.890489 TCCGACTCGTTGAAGATGGAA 59.110 47.619 0.00 0.00 0.00 3.53 R
2697 2774 2.284625 TGGATGGTCGCCTCCAGT 60.285 61.111 10.61 0.00 41.05 4.00 R
3748 3961 0.033504 TCGAACTCACCAGGCTGTTC 59.966 55.000 14.43 9.07 36.44 3.18 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
38 39 7.409449 CGATCTAAGTAAAACGTGTCTCTGTTG 60.409 40.741 0.00 0.00 0.00 3.33
51 52 0.908910 TCTGTTGGGCATACGGATGT 59.091 50.000 9.90 0.00 35.30 3.06
55 56 0.395036 TTGGGCATACGGATGTTGGG 60.395 55.000 9.90 0.00 35.30 4.12
56 57 2.193536 GGGCATACGGATGTTGGGC 61.194 63.158 9.90 0.00 35.30 5.36
83 84 4.368391 GGCATAGCCTCCGTCATG 57.632 61.111 0.00 0.00 46.69 3.07
86 87 1.302033 CATAGCCTCCGTCATGCCC 60.302 63.158 0.00 0.00 0.00 5.36
94 95 4.418328 CGTCATGCCCGGGGGAAA 62.418 66.667 25.28 0.00 37.50 3.13
95 96 2.278738 GTCATGCCCGGGGGAAAT 59.721 61.111 25.28 0.00 37.50 2.17
96 97 2.127232 GTCATGCCCGGGGGAAATG 61.127 63.158 25.28 6.60 37.50 2.32
97 98 2.278404 CATGCCCGGGGGAAATGA 59.722 61.111 25.28 0.00 37.50 2.57
107 108 2.799207 CGGGGGAAATGAAAATGATGCG 60.799 50.000 0.00 0.00 0.00 4.73
117 118 4.592192 ATGATGCGCCGGTCGAGG 62.592 66.667 20.06 0.00 41.67 4.63
126 127 4.227134 CGGTCGAGGCCCTGGATG 62.227 72.222 0.00 0.00 0.00 3.51
127 128 2.764128 GGTCGAGGCCCTGGATGA 60.764 66.667 0.00 0.00 0.00 2.92
128 129 2.143419 GGTCGAGGCCCTGGATGAT 61.143 63.158 0.00 0.00 0.00 2.45
129 130 0.832135 GGTCGAGGCCCTGGATGATA 60.832 60.000 0.00 0.00 0.00 2.15
130 131 1.270907 GTCGAGGCCCTGGATGATAT 58.729 55.000 0.00 0.00 0.00 1.63
131 132 1.625818 GTCGAGGCCCTGGATGATATT 59.374 52.381 0.00 0.00 0.00 1.28
132 133 2.039084 GTCGAGGCCCTGGATGATATTT 59.961 50.000 0.00 0.00 0.00 1.40
133 134 2.711009 TCGAGGCCCTGGATGATATTTT 59.289 45.455 0.00 0.00 0.00 1.82
134 135 3.077359 CGAGGCCCTGGATGATATTTTC 58.923 50.000 0.00 0.00 0.00 2.29
135 136 3.077359 GAGGCCCTGGATGATATTTTCG 58.923 50.000 0.00 0.00 0.00 3.46
136 137 2.162681 GGCCCTGGATGATATTTTCGG 58.837 52.381 0.00 0.00 0.00 4.30
137 138 1.541588 GCCCTGGATGATATTTTCGGC 59.458 52.381 0.00 0.00 0.00 5.54
138 139 2.162681 CCCTGGATGATATTTTCGGCC 58.837 52.381 0.00 0.00 0.00 6.13
139 140 1.806542 CCTGGATGATATTTTCGGCCG 59.193 52.381 22.12 22.12 0.00 6.13
140 141 2.549992 CCTGGATGATATTTTCGGCCGA 60.550 50.000 27.28 27.28 0.00 5.54
141 142 2.480419 CTGGATGATATTTTCGGCCGAC 59.520 50.000 31.19 16.32 0.00 4.79
142 143 2.104111 TGGATGATATTTTCGGCCGACT 59.896 45.455 31.19 18.14 0.00 4.18
143 144 2.480419 GGATGATATTTTCGGCCGACTG 59.520 50.000 31.19 0.00 0.00 3.51
352 371 1.603172 CGAGCTACATCAACGGGGATC 60.603 57.143 0.00 0.00 0.00 3.36
412 433 5.750547 CAGAGTTGAGCGAAAATATCTGCTA 59.249 40.000 0.00 0.00 37.80 3.49
559 580 2.057316 CGATCGATAGTCGGTACTCGT 58.943 52.381 10.26 0.00 40.88 4.18
563 584 1.576356 GATAGTCGGTACTCGTCCGT 58.424 55.000 4.36 0.00 46.86 4.69
567 588 1.742880 TCGGTACTCGTCCGTCCTG 60.743 63.158 4.36 0.00 46.86 3.86
592 613 4.926832 TGTTACCTGTCGACACATGTTATG 59.073 41.667 15.76 1.86 33.77 1.90
624 646 2.959030 AGGGAAGAAAAGCCAACAAGAC 59.041 45.455 0.00 0.00 0.00 3.01
642 667 2.428071 GACGCAGCAGCAGCAAAC 60.428 61.111 10.77 0.00 45.49 2.93
643 668 4.318021 ACGCAGCAGCAGCAAACG 62.318 61.111 10.77 6.37 45.49 3.60
646 671 2.979676 CAGCAGCAGCAAACGGGA 60.980 61.111 3.17 0.00 45.49 5.14
647 672 2.670934 AGCAGCAGCAAACGGGAG 60.671 61.111 3.17 0.00 45.49 4.30
734 759 2.348998 CCACTCCTCCCAGTGTGC 59.651 66.667 0.22 0.00 42.10 4.57
745 772 1.669115 CAGTGTGCGAGTCCTTGGG 60.669 63.158 0.00 0.00 0.00 4.12
748 775 1.911269 TGTGCGAGTCCTTGGGCTA 60.911 57.895 0.00 0.00 0.00 3.93
785 826 1.068083 CCACACTCCCATCGATCCG 59.932 63.158 0.00 0.00 0.00 4.18
802 843 1.068895 TCCGTCTCTTTTACCAACGCA 59.931 47.619 0.00 0.00 32.26 5.24
857 904 5.504337 GCTCCAACTCTATATATACGCTCGG 60.504 48.000 0.00 0.00 0.00 4.63
886 933 2.422519 GCTCCAGACATCAACCATCCAT 60.423 50.000 0.00 0.00 0.00 3.41
984 1046 3.587933 GACTCTCGCCGCGATCCT 61.588 66.667 17.22 0.63 34.61 3.24
1284 1355 2.754658 GACGCCTTCGAGGAGGGA 60.755 66.667 5.32 0.00 39.71 4.20
1638 1709 4.615815 GCCATCGGCGAGCTCCAT 62.616 66.667 17.22 0.00 39.62 3.41
1770 1841 2.362369 CCACCTCCTCGCCATGTCT 61.362 63.158 0.00 0.00 0.00 3.41
1797 1868 2.361610 ATCCCGTACCACGTCCGT 60.362 61.111 0.00 0.00 40.58 4.69
1956 2027 5.145513 AGCCCTACCTCAAGTACTTCTAT 57.854 43.478 4.77 0.00 0.00 1.98
2875 2952 3.521531 GGAGGAGATGGAAAGAGGAAGTT 59.478 47.826 0.00 0.00 0.00 2.66
2935 3012 0.846693 ATCTTCCCTTCCATTCCCCG 59.153 55.000 0.00 0.00 0.00 5.73
2940 3017 2.045045 CTTCCATTCCCCGCTGCA 60.045 61.111 0.00 0.00 0.00 4.41
2993 3087 1.800805 TAGCTCACACTTGCTTCAGC 58.199 50.000 0.00 0.00 40.35 4.26
3046 3140 4.469945 AGTAAAACCTAGCTGCCACTCATA 59.530 41.667 0.00 0.00 0.00 2.15
3050 3144 1.759445 CCTAGCTGCCACTCATAGTGT 59.241 52.381 0.00 0.00 44.50 3.55
3054 3148 1.633561 CTGCCACTCATAGTGTCACG 58.366 55.000 6.33 0.00 44.50 4.35
3058 3152 1.182667 CACTCATAGTGTCACGGGGA 58.817 55.000 0.00 0.00 41.19 4.81
3077 3171 4.775253 GGGGAAGTGAGGATTAGAGATAGG 59.225 50.000 0.00 0.00 0.00 2.57
3078 3172 5.399113 GGGAAGTGAGGATTAGAGATAGGT 58.601 45.833 0.00 0.00 0.00 3.08
3079 3173 6.468945 GGGGAAGTGAGGATTAGAGATAGGTA 60.469 46.154 0.00 0.00 0.00 3.08
3080 3174 6.661805 GGGAAGTGAGGATTAGAGATAGGTAG 59.338 46.154 0.00 0.00 0.00 3.18
3081 3175 7.463431 GGAAGTGAGGATTAGAGATAGGTAGA 58.537 42.308 0.00 0.00 0.00 2.59
3082 3176 7.610305 GGAAGTGAGGATTAGAGATAGGTAGAG 59.390 44.444 0.00 0.00 0.00 2.43
3083 3177 7.881912 AGTGAGGATTAGAGATAGGTAGAGA 57.118 40.000 0.00 0.00 0.00 3.10
3084 3178 7.918076 AGTGAGGATTAGAGATAGGTAGAGAG 58.082 42.308 0.00 0.00 0.00 3.20
3085 3179 7.737607 AGTGAGGATTAGAGATAGGTAGAGAGA 59.262 40.741 0.00 0.00 0.00 3.10
3086 3180 8.041323 GTGAGGATTAGAGATAGGTAGAGAGAG 58.959 44.444 0.00 0.00 0.00 3.20
3087 3181 7.959152 TGAGGATTAGAGATAGGTAGAGAGAGA 59.041 40.741 0.00 0.00 0.00 3.10
3088 3182 8.380742 AGGATTAGAGATAGGTAGAGAGAGAG 57.619 42.308 0.00 0.00 0.00 3.20
3089 3183 7.403231 AGGATTAGAGATAGGTAGAGAGAGAGG 59.597 44.444 0.00 0.00 0.00 3.69
3113 3207 3.378399 GAAGAGGGGTCCAGCTCGC 62.378 68.421 0.00 0.00 0.00 5.03
3222 3321 5.355630 TCATTTTATCACACGGGTTGGTATG 59.644 40.000 0.00 0.00 0.00 2.39
3223 3322 2.319136 TATCACACGGGTTGGTATGC 57.681 50.000 0.00 0.00 0.00 3.14
3244 3348 2.286184 CGTACAAATATGCTCCGGTTGC 60.286 50.000 13.68 13.68 0.00 4.17
3388 3601 0.172352 ATTGGCGCCCATGTAAAACG 59.828 50.000 26.77 0.00 31.53 3.60
3430 3643 8.539770 TCTGCTCTGTCAGTAAAAGATAAAAG 57.460 34.615 0.00 0.00 35.63 2.27
3457 3670 0.726827 GATTGATCCGTTGCTGCGAA 59.273 50.000 0.00 0.00 0.00 4.70
3472 3685 3.859627 GCTGCGAAGTACAGTAGTCCAAA 60.860 47.826 0.00 0.00 37.47 3.28
3487 3700 3.712016 TCCAAATTGGATGAACCGAGA 57.288 42.857 11.23 0.00 42.67 4.04
3515 3728 0.608035 TGCTTCTAGGCGTTTTGGGG 60.608 55.000 0.00 0.00 34.52 4.96
3527 3740 1.771854 GTTTTGGGGTTGAAATGGGGT 59.228 47.619 0.00 0.00 0.00 4.95
3532 3745 0.608130 GGGTTGAAATGGGGTCTTGC 59.392 55.000 0.00 0.00 0.00 4.01
3586 3799 4.415332 CCCGTCCGTCAGTCCGTG 62.415 72.222 0.00 0.00 0.00 4.94
3587 3800 4.415332 CCGTCCGTCAGTCCGTGG 62.415 72.222 0.00 0.00 0.00 4.94
3588 3801 4.415332 CGTCCGTCAGTCCGTGGG 62.415 72.222 0.00 0.00 0.00 4.61
3589 3802 4.736896 GTCCGTCAGTCCGTGGGC 62.737 72.222 0.00 0.00 0.00 5.36
3593 3806 3.771160 GTCAGTCCGTGGGCCGAT 61.771 66.667 0.00 0.00 39.56 4.18
3594 3807 3.770040 TCAGTCCGTGGGCCGATG 61.770 66.667 0.00 0.00 39.56 3.84
3595 3808 4.082523 CAGTCCGTGGGCCGATGT 62.083 66.667 6.20 0.00 39.56 3.06
3596 3809 4.082523 AGTCCGTGGGCCGATGTG 62.083 66.667 6.20 0.00 39.56 3.21
3597 3810 4.388499 GTCCGTGGGCCGATGTGT 62.388 66.667 6.20 0.00 39.56 3.72
3598 3811 4.386951 TCCGTGGGCCGATGTGTG 62.387 66.667 6.20 0.00 39.56 3.82
3599 3812 4.697756 CCGTGGGCCGATGTGTGT 62.698 66.667 6.20 0.00 39.56 3.72
3600 3813 2.263227 CGTGGGCCGATGTGTGTA 59.737 61.111 0.00 0.00 39.56 2.90
3601 3814 2.098233 CGTGGGCCGATGTGTGTAC 61.098 63.158 0.00 0.00 39.56 2.90
3602 3815 1.004320 GTGGGCCGATGTGTGTACA 60.004 57.895 0.00 0.00 41.89 2.90
3603 3816 1.019278 GTGGGCCGATGTGTGTACAG 61.019 60.000 0.00 0.00 40.79 2.74
3604 3817 1.449601 GGGCCGATGTGTGTACAGG 60.450 63.158 0.00 0.00 40.79 4.00
3605 3818 2.106683 GGCCGATGTGTGTACAGGC 61.107 63.158 12.01 12.01 43.69 4.85
3606 3819 2.452813 GCCGATGTGTGTACAGGCG 61.453 63.158 5.87 1.69 38.07 5.52
3607 3820 1.214325 CCGATGTGTGTACAGGCGA 59.786 57.895 0.00 0.00 40.79 5.54
3608 3821 0.802222 CCGATGTGTGTACAGGCGAG 60.802 60.000 0.00 0.00 40.79 5.03
3609 3822 0.170339 CGATGTGTGTACAGGCGAGA 59.830 55.000 0.00 0.00 40.79 4.04
3610 3823 1.795525 CGATGTGTGTACAGGCGAGAG 60.796 57.143 0.00 0.00 40.79 3.20
3611 3824 0.532573 ATGTGTGTACAGGCGAGAGG 59.467 55.000 0.00 0.00 40.79 3.69
3612 3825 0.826256 TGTGTGTACAGGCGAGAGGT 60.826 55.000 0.00 0.00 31.91 3.85
3613 3826 0.388649 GTGTGTACAGGCGAGAGGTG 60.389 60.000 0.00 0.00 0.00 4.00
3614 3827 1.215647 GTGTACAGGCGAGAGGTGG 59.784 63.158 0.00 0.00 0.00 4.61
3615 3828 1.076014 TGTACAGGCGAGAGGTGGA 59.924 57.895 0.00 0.00 0.00 4.02
3616 3829 1.248785 TGTACAGGCGAGAGGTGGAC 61.249 60.000 0.00 0.00 0.00 4.02
3617 3830 2.044555 TACAGGCGAGAGGTGGACG 61.045 63.158 0.00 0.00 0.00 4.79
3622 3835 2.962569 CGAGAGGTGGACGCTGAA 59.037 61.111 0.00 0.00 0.00 3.02
3623 3836 1.513158 CGAGAGGTGGACGCTGAAT 59.487 57.895 0.00 0.00 0.00 2.57
3624 3837 0.526524 CGAGAGGTGGACGCTGAATC 60.527 60.000 0.00 0.00 0.00 2.52
3625 3838 0.820871 GAGAGGTGGACGCTGAATCT 59.179 55.000 0.00 0.00 0.00 2.40
3626 3839 0.534412 AGAGGTGGACGCTGAATCTG 59.466 55.000 0.00 0.00 0.00 2.90
3627 3840 0.532573 GAGGTGGACGCTGAATCTGA 59.467 55.000 0.00 0.00 0.00 3.27
3628 3841 1.137872 GAGGTGGACGCTGAATCTGAT 59.862 52.381 0.00 0.00 0.00 2.90
3629 3842 1.137872 AGGTGGACGCTGAATCTGATC 59.862 52.381 0.00 0.00 0.00 2.92
3630 3843 1.134699 GGTGGACGCTGAATCTGATCA 60.135 52.381 0.00 0.00 0.00 2.92
3632 3845 1.137675 TGGACGCTGAATCTGATCAGG 59.862 52.381 22.42 7.19 45.60 3.86
3641 3854 6.910995 GCTGAATCTGATCAGGGAAATATTG 58.089 40.000 22.42 4.63 45.60 1.90
3642 3855 6.713903 GCTGAATCTGATCAGGGAAATATTGA 59.286 38.462 22.42 7.14 45.60 2.57
3643 3856 7.094720 GCTGAATCTGATCAGGGAAATATTGAG 60.095 40.741 22.42 16.22 45.60 3.02
3644 3857 6.713903 TGAATCTGATCAGGGAAATATTGAGC 59.286 38.462 22.42 3.51 0.00 4.26
3645 3858 4.635223 TCTGATCAGGGAAATATTGAGCG 58.365 43.478 22.42 0.00 30.26 5.03
3646 3859 4.344968 TCTGATCAGGGAAATATTGAGCGA 59.655 41.667 22.42 0.00 30.26 4.93
3647 3860 4.635223 TGATCAGGGAAATATTGAGCGAG 58.365 43.478 0.00 0.00 30.26 5.03
3648 3861 2.838736 TCAGGGAAATATTGAGCGAGC 58.161 47.619 0.00 0.00 0.00 5.03
3649 3862 2.435805 TCAGGGAAATATTGAGCGAGCT 59.564 45.455 0.00 0.00 0.00 4.09
3650 3863 2.547211 CAGGGAAATATTGAGCGAGCTG 59.453 50.000 0.84 0.00 0.00 4.24
3651 3864 2.171448 AGGGAAATATTGAGCGAGCTGT 59.829 45.455 0.84 0.00 0.00 4.40
3652 3865 2.289002 GGGAAATATTGAGCGAGCTGTG 59.711 50.000 0.84 0.00 0.00 3.66
3653 3866 2.939103 GGAAATATTGAGCGAGCTGTGT 59.061 45.455 0.84 0.00 0.00 3.72
3654 3867 3.375299 GGAAATATTGAGCGAGCTGTGTT 59.625 43.478 0.84 0.00 0.00 3.32
3655 3868 4.337763 GAAATATTGAGCGAGCTGTGTTG 58.662 43.478 0.84 0.00 0.00 3.33
3656 3869 2.455674 TATTGAGCGAGCTGTGTTGT 57.544 45.000 0.84 0.00 0.00 3.32
3657 3870 1.151668 ATTGAGCGAGCTGTGTTGTC 58.848 50.000 0.84 0.00 0.00 3.18
3658 3871 0.104855 TTGAGCGAGCTGTGTTGTCT 59.895 50.000 0.84 0.00 0.00 3.41
3659 3872 0.319040 TGAGCGAGCTGTGTTGTCTC 60.319 55.000 0.84 0.00 0.00 3.36
3660 3873 0.038709 GAGCGAGCTGTGTTGTCTCT 60.039 55.000 0.84 0.00 0.00 3.10
3661 3874 0.319383 AGCGAGCTGTGTTGTCTCTG 60.319 55.000 0.00 0.00 0.00 3.35
3662 3875 0.598680 GCGAGCTGTGTTGTCTCTGT 60.599 55.000 0.00 0.00 0.00 3.41
3663 3876 1.858091 CGAGCTGTGTTGTCTCTGTT 58.142 50.000 0.00 0.00 0.00 3.16
3664 3877 1.524355 CGAGCTGTGTTGTCTCTGTTG 59.476 52.381 0.00 0.00 0.00 3.33
3665 3878 2.555199 GAGCTGTGTTGTCTCTGTTGT 58.445 47.619 0.00 0.00 0.00 3.32
3666 3879 2.283298 AGCTGTGTTGTCTCTGTTGTG 58.717 47.619 0.00 0.00 0.00 3.33
3667 3880 1.331756 GCTGTGTTGTCTCTGTTGTGG 59.668 52.381 0.00 0.00 0.00 4.17
3668 3881 2.905075 CTGTGTTGTCTCTGTTGTGGA 58.095 47.619 0.00 0.00 0.00 4.02
3669 3882 2.868583 CTGTGTTGTCTCTGTTGTGGAG 59.131 50.000 0.00 0.00 0.00 3.86
3670 3883 1.599542 GTGTTGTCTCTGTTGTGGAGC 59.400 52.381 0.00 0.00 0.00 4.70
3671 3884 1.486310 TGTTGTCTCTGTTGTGGAGCT 59.514 47.619 0.00 0.00 0.00 4.09
3672 3885 2.092968 TGTTGTCTCTGTTGTGGAGCTT 60.093 45.455 0.00 0.00 0.00 3.74
3673 3886 2.945668 GTTGTCTCTGTTGTGGAGCTTT 59.054 45.455 0.00 0.00 0.00 3.51
3674 3887 2.564771 TGTCTCTGTTGTGGAGCTTTG 58.435 47.619 0.00 0.00 0.00 2.77
3675 3888 2.092968 TGTCTCTGTTGTGGAGCTTTGT 60.093 45.455 0.00 0.00 0.00 2.83
3676 3889 2.945668 GTCTCTGTTGTGGAGCTTTGTT 59.054 45.455 0.00 0.00 0.00 2.83
3677 3890 3.378427 GTCTCTGTTGTGGAGCTTTGTTT 59.622 43.478 0.00 0.00 0.00 2.83
3678 3891 3.627577 TCTCTGTTGTGGAGCTTTGTTTC 59.372 43.478 0.00 0.00 0.00 2.78
3679 3892 2.687935 TCTGTTGTGGAGCTTTGTTTCC 59.312 45.455 0.00 0.00 0.00 3.13
3680 3893 1.754226 TGTTGTGGAGCTTTGTTTCCC 59.246 47.619 0.00 0.00 32.29 3.97
3681 3894 2.031870 GTTGTGGAGCTTTGTTTCCCT 58.968 47.619 0.00 0.00 32.29 4.20
3682 3895 2.430694 GTTGTGGAGCTTTGTTTCCCTT 59.569 45.455 0.00 0.00 32.29 3.95
3683 3896 2.031120 TGTGGAGCTTTGTTTCCCTTG 58.969 47.619 0.00 0.00 32.29 3.61
3684 3897 1.039856 TGGAGCTTTGTTTCCCTTGC 58.960 50.000 0.00 0.00 32.29 4.01
3685 3898 1.039856 GGAGCTTTGTTTCCCTTGCA 58.960 50.000 0.00 0.00 0.00 4.08
3686 3899 1.620323 GGAGCTTTGTTTCCCTTGCAT 59.380 47.619 0.00 0.00 0.00 3.96
3687 3900 2.825532 GGAGCTTTGTTTCCCTTGCATA 59.174 45.455 0.00 0.00 0.00 3.14
3688 3901 3.258123 GGAGCTTTGTTTCCCTTGCATAA 59.742 43.478 0.00 0.00 0.00 1.90
3689 3902 4.081476 GGAGCTTTGTTTCCCTTGCATAAT 60.081 41.667 0.00 0.00 0.00 1.28
3690 3903 5.482006 GAGCTTTGTTTCCCTTGCATAATT 58.518 37.500 0.00 0.00 0.00 1.40
3691 3904 5.868454 AGCTTTGTTTCCCTTGCATAATTT 58.132 33.333 0.00 0.00 0.00 1.82
3692 3905 5.934043 AGCTTTGTTTCCCTTGCATAATTTC 59.066 36.000 0.00 0.00 0.00 2.17
3693 3906 5.700373 GCTTTGTTTCCCTTGCATAATTTCA 59.300 36.000 0.00 0.00 0.00 2.69
3694 3907 6.372381 GCTTTGTTTCCCTTGCATAATTTCAT 59.628 34.615 0.00 0.00 0.00 2.57
3695 3908 7.548780 GCTTTGTTTCCCTTGCATAATTTCATA 59.451 33.333 0.00 0.00 0.00 2.15
3696 3909 8.770438 TTTGTTTCCCTTGCATAATTTCATAC 57.230 30.769 0.00 0.00 0.00 2.39
3697 3910 7.716799 TGTTTCCCTTGCATAATTTCATACT 57.283 32.000 0.00 0.00 0.00 2.12
3698 3911 8.815565 TGTTTCCCTTGCATAATTTCATACTA 57.184 30.769 0.00 0.00 0.00 1.82
3699 3912 8.682710 TGTTTCCCTTGCATAATTTCATACTAC 58.317 33.333 0.00 0.00 0.00 2.73
3700 3913 7.490962 TTCCCTTGCATAATTTCATACTACG 57.509 36.000 0.00 0.00 0.00 3.51
3701 3914 6.588204 TCCCTTGCATAATTTCATACTACGT 58.412 36.000 0.00 0.00 0.00 3.57
3702 3915 7.728148 TCCCTTGCATAATTTCATACTACGTA 58.272 34.615 0.00 0.00 0.00 3.57
3703 3916 7.654520 TCCCTTGCATAATTTCATACTACGTAC 59.345 37.037 0.00 0.00 0.00 3.67
3704 3917 7.656137 CCCTTGCATAATTTCATACTACGTACT 59.344 37.037 0.00 0.00 0.00 2.73
3705 3918 8.487970 CCTTGCATAATTTCATACTACGTACTG 58.512 37.037 0.00 0.00 0.00 2.74
3706 3919 7.402811 TGCATAATTTCATACTACGTACTGC 57.597 36.000 0.00 0.00 0.00 4.40
3720 3933 3.999229 GTACTGCGTACGTACTACAGT 57.001 47.619 34.15 34.15 41.24 3.55
3722 3935 5.643339 GTACTGCGTACGTACTACAGTAT 57.357 43.478 35.51 24.21 41.34 2.12
3723 3936 4.526970 ACTGCGTACGTACTACAGTATG 57.473 45.455 32.60 18.45 38.58 2.39
3725 3938 6.455646 GTACTGCGTACGTACTACAGTATGTT 60.456 42.308 35.51 23.30 45.54 2.71
3726 3939 8.187900 GTACTGCGTACGTACTACAGTATGTTC 61.188 44.444 35.51 26.69 45.54 3.18
3741 3954 6.825584 CAGTATGTTCCAGATATGATTTCGC 58.174 40.000 0.00 0.00 0.00 4.70
3742 3955 5.934625 AGTATGTTCCAGATATGATTTCGCC 59.065 40.000 0.00 0.00 0.00 5.54
3743 3956 3.130633 TGTTCCAGATATGATTTCGCCG 58.869 45.455 0.00 0.00 0.00 6.46
3744 3957 1.795768 TCCAGATATGATTTCGCCGC 58.204 50.000 0.00 0.00 0.00 6.53
3745 3958 1.069978 TCCAGATATGATTTCGCCGCA 59.930 47.619 0.00 0.00 0.00 5.69
3746 3959 1.872952 CCAGATATGATTTCGCCGCAA 59.127 47.619 0.00 0.00 0.00 4.85
3747 3960 2.096069 CCAGATATGATTTCGCCGCAAG 60.096 50.000 0.00 0.00 0.00 4.01
3765 3978 2.934083 GGAACAGCCTGGTGAGTTC 58.066 57.895 15.12 15.12 39.59 3.01
3766 3979 0.951040 GGAACAGCCTGGTGAGTTCG 60.951 60.000 16.19 0.00 40.83 3.95
3767 3980 0.033504 GAACAGCCTGGTGAGTTCGA 59.966 55.000 2.95 0.00 32.17 3.71
3768 3981 0.468226 AACAGCCTGGTGAGTTCGAA 59.532 50.000 2.95 0.00 0.00 3.71
3769 3982 0.034059 ACAGCCTGGTGAGTTCGAAG 59.966 55.000 0.00 0.00 0.00 3.79
3770 3983 1.004440 AGCCTGGTGAGTTCGAAGC 60.004 57.895 0.00 0.00 0.00 3.86
3771 3984 2.383527 GCCTGGTGAGTTCGAAGCG 61.384 63.158 0.00 0.00 0.00 4.68
3772 3985 1.006102 CCTGGTGAGTTCGAAGCGT 60.006 57.895 0.00 0.00 0.00 5.07
3773 3986 0.242825 CCTGGTGAGTTCGAAGCGTA 59.757 55.000 0.00 0.00 0.00 4.42
3774 3987 1.618861 CTGGTGAGTTCGAAGCGTAG 58.381 55.000 0.00 0.00 0.00 3.51
3775 3988 0.956633 TGGTGAGTTCGAAGCGTAGT 59.043 50.000 0.00 0.00 0.00 2.73
3776 3989 1.068748 TGGTGAGTTCGAAGCGTAGTC 60.069 52.381 0.00 0.00 0.00 2.59
3777 3990 1.248721 GTGAGTTCGAAGCGTAGTCG 58.751 55.000 0.00 0.00 39.88 4.18
3778 3991 0.870393 TGAGTTCGAAGCGTAGTCGT 59.130 50.000 0.00 0.00 39.52 4.34
3779 3992 1.248721 GAGTTCGAAGCGTAGTCGTG 58.751 55.000 0.00 0.00 39.52 4.35
3780 3993 0.109873 AGTTCGAAGCGTAGTCGTGG 60.110 55.000 0.00 0.00 39.52 4.94
3781 3994 0.110056 GTTCGAAGCGTAGTCGTGGA 60.110 55.000 0.00 0.00 39.52 4.02
3782 3995 0.806868 TTCGAAGCGTAGTCGTGGAT 59.193 50.000 0.00 0.00 39.52 3.41
3783 3996 0.098200 TCGAAGCGTAGTCGTGGATG 59.902 55.000 4.82 0.00 39.52 3.51
3784 3997 1.472276 CGAAGCGTAGTCGTGGATGC 61.472 60.000 0.00 0.00 39.49 3.91
3785 3998 0.457853 GAAGCGTAGTCGTGGATGCA 60.458 55.000 0.00 0.00 39.49 3.96
3786 3999 0.736325 AAGCGTAGTCGTGGATGCAC 60.736 55.000 7.39 7.39 39.49 4.57
3787 4000 2.165301 GCGTAGTCGTGGATGCACC 61.165 63.158 12.15 0.00 39.49 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.534778 GTTTTACTTAGATCGTATAAACCGTGG 58.465 37.037 0.00 0.00 0.00 4.94
1 2 8.255143 CGTTTTACTTAGATCGTATAAACCGTG 58.745 37.037 0.00 0.00 0.00 4.94
2 3 7.968405 ACGTTTTACTTAGATCGTATAAACCGT 59.032 33.333 9.71 9.71 0.00 4.83
3 4 8.255143 CACGTTTTACTTAGATCGTATAAACCG 58.745 37.037 0.00 8.84 0.00 4.44
4 5 9.076596 ACACGTTTTACTTAGATCGTATAAACC 57.923 33.333 0.00 0.00 0.00 3.27
38 39 2.193536 GCCCAACATCCGTATGCCC 61.194 63.158 0.00 0.00 36.50 5.36
55 56 2.348998 CTATGCCAGGGGGATCGC 59.651 66.667 0.06 0.06 34.92 4.58
56 57 2.348998 GCTATGCCAGGGGGATCG 59.651 66.667 0.00 0.00 34.92 3.69
80 81 0.975040 TTTCATTTCCCCCGGGCATG 60.975 55.000 17.73 14.03 34.68 4.06
82 83 0.252467 ATTTTCATTTCCCCCGGGCA 60.252 50.000 17.73 0.00 34.68 5.36
83 84 0.177836 CATTTTCATTTCCCCCGGGC 59.822 55.000 17.73 0.00 34.68 6.13
86 87 2.799207 CGCATCATTTTCATTTCCCCCG 60.799 50.000 0.00 0.00 0.00 5.73
90 91 1.854126 CGGCGCATCATTTTCATTTCC 59.146 47.619 10.83 0.00 0.00 3.13
91 92 1.854126 CCGGCGCATCATTTTCATTTC 59.146 47.619 10.83 0.00 0.00 2.17
92 93 1.204467 ACCGGCGCATCATTTTCATTT 59.796 42.857 10.83 0.00 0.00 2.32
93 94 0.817013 ACCGGCGCATCATTTTCATT 59.183 45.000 10.83 0.00 0.00 2.57
94 95 0.381801 GACCGGCGCATCATTTTCAT 59.618 50.000 10.83 0.00 0.00 2.57
95 96 1.800032 GACCGGCGCATCATTTTCA 59.200 52.632 10.83 0.00 0.00 2.69
96 97 1.297598 CGACCGGCGCATCATTTTC 60.298 57.895 10.83 0.00 0.00 2.29
97 98 1.705337 CTCGACCGGCGCATCATTTT 61.705 55.000 10.83 0.00 40.61 1.82
117 118 1.541588 GCCGAAAATATCATCCAGGGC 59.458 52.381 0.00 0.00 0.00 5.19
119 120 1.806542 CGGCCGAAAATATCATCCAGG 59.193 52.381 24.07 0.00 0.00 4.45
120 121 2.480419 GTCGGCCGAAAATATCATCCAG 59.520 50.000 32.93 0.00 0.00 3.86
122 123 2.480419 CAGTCGGCCGAAAATATCATCC 59.520 50.000 32.93 13.52 0.00 3.51
123 124 2.096218 GCAGTCGGCCGAAAATATCATC 60.096 50.000 32.93 14.35 36.11 2.92
125 126 1.295792 GCAGTCGGCCGAAAATATCA 58.704 50.000 32.93 0.83 36.11 2.15
126 127 0.232303 CGCAGTCGGCCGAAAATATC 59.768 55.000 32.93 16.85 40.31 1.63
127 128 0.179094 TCGCAGTCGGCCGAAAATAT 60.179 50.000 32.93 10.96 40.31 1.28
128 129 1.079875 GTCGCAGTCGGCCGAAAATA 61.080 55.000 32.93 12.07 40.31 1.40
129 130 2.047655 TCGCAGTCGGCCGAAAAT 60.048 55.556 32.93 16.67 40.31 1.82
130 131 3.039588 GTCGCAGTCGGCCGAAAA 61.040 61.111 32.93 10.86 40.31 2.29
156 157 3.764049 GGCACAACGCTCGTCGAC 61.764 66.667 5.18 5.18 41.67 4.20
352 371 7.042797 ACCATTAGCAGCATAATTAAACAGG 57.957 36.000 0.00 0.00 0.00 4.00
559 580 0.830444 ACAGGTAACAGCAGGACGGA 60.830 55.000 0.00 0.00 41.41 4.69
562 583 0.601558 TCGACAGGTAACAGCAGGAC 59.398 55.000 0.00 0.00 41.41 3.85
563 584 0.601558 GTCGACAGGTAACAGCAGGA 59.398 55.000 11.55 0.00 41.41 3.86
567 588 1.726791 CATGTGTCGACAGGTAACAGC 59.273 52.381 20.73 4.95 34.87 4.40
624 646 4.016629 TTTGCTGCTGCTGCGTCG 62.017 61.111 23.38 3.28 43.34 5.12
734 759 2.901042 GGGTAGCCCAAGGACTCG 59.099 66.667 0.00 0.00 44.65 4.18
745 772 1.293963 GACGGTTTGAACGGGGTAGC 61.294 60.000 6.42 0.00 33.99 3.58
748 775 2.111669 GGACGGTTTGAACGGGGT 59.888 61.111 6.42 0.00 33.99 4.95
785 826 2.899977 CGTTGCGTTGGTAAAAGAGAC 58.100 47.619 0.00 0.00 0.00 3.36
825 872 4.785453 GAGTTGGAGCAGGGCGGG 62.785 72.222 0.00 0.00 0.00 6.13
826 873 1.690219 ATAGAGTTGGAGCAGGGCGG 61.690 60.000 0.00 0.00 0.00 6.13
827 874 1.040646 TATAGAGTTGGAGCAGGGCG 58.959 55.000 0.00 0.00 0.00 6.13
828 875 5.450688 CGTATATATAGAGTTGGAGCAGGGC 60.451 48.000 0.00 0.00 0.00 5.19
829 876 5.450688 GCGTATATATAGAGTTGGAGCAGGG 60.451 48.000 0.00 0.00 0.00 4.45
832 879 5.064834 CGAGCGTATATATAGAGTTGGAGCA 59.935 44.000 0.00 0.00 0.00 4.26
857 904 2.362329 GATGTCTGGAGCTCGGAGGC 62.362 65.000 7.83 8.31 0.00 4.70
1770 1841 1.033746 GGTACGGGATGTCGTCCTCA 61.034 60.000 10.99 0.00 46.91 3.86
1905 1976 3.428282 TCGTAGCTGAGCGCGTGA 61.428 61.111 19.71 6.08 45.59 4.35
2289 2360 1.890489 TCCGACTCGTTGAAGATGGAA 59.110 47.619 0.00 0.00 0.00 3.53
2697 2774 2.284625 TGGATGGTCGCCTCCAGT 60.285 61.111 10.61 0.00 41.05 4.00
2949 3026 6.282167 ACTGAATATGAACAGAGATGAGCTG 58.718 40.000 0.00 0.00 37.54 4.24
3046 3140 1.472662 CCTCACTTCCCCGTGACACT 61.473 60.000 3.68 0.00 38.89 3.55
3050 3144 2.108168 CTAATCCTCACTTCCCCGTGA 58.892 52.381 0.00 0.00 41.33 4.35
3054 3148 4.775253 CCTATCTCTAATCCTCACTTCCCC 59.225 50.000 0.00 0.00 0.00 4.81
3058 3152 8.282801 TCTCTACCTATCTCTAATCCTCACTT 57.717 38.462 0.00 0.00 0.00 3.16
3077 3171 3.714798 TCTTCCTCTCCCTCTCTCTCTAC 59.285 52.174 0.00 0.00 0.00 2.59
3078 3172 3.973973 CTCTTCCTCTCCCTCTCTCTCTA 59.026 52.174 0.00 0.00 0.00 2.43
3079 3173 2.780010 CTCTTCCTCTCCCTCTCTCTCT 59.220 54.545 0.00 0.00 0.00 3.10
3080 3174 2.158608 CCTCTTCCTCTCCCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
3081 3175 1.852965 CCTCTTCCTCTCCCTCTCTCT 59.147 57.143 0.00 0.00 0.00 3.10
3082 3176 1.133482 CCCTCTTCCTCTCCCTCTCTC 60.133 61.905 0.00 0.00 0.00 3.20
3083 3177 0.933700 CCCTCTTCCTCTCCCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
3084 3178 0.105709 CCCCTCTTCCTCTCCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
3085 3179 0.858139 ACCCCTCTTCCTCTCCCTCT 60.858 60.000 0.00 0.00 0.00 3.69
3086 3180 0.397957 GACCCCTCTTCCTCTCCCTC 60.398 65.000 0.00 0.00 0.00 4.30
3087 3181 1.707200 GACCCCTCTTCCTCTCCCT 59.293 63.158 0.00 0.00 0.00 4.20
3088 3182 1.383386 GGACCCCTCTTCCTCTCCC 60.383 68.421 0.00 0.00 0.00 4.30
3089 3183 0.689412 CTGGACCCCTCTTCCTCTCC 60.689 65.000 0.00 0.00 33.84 3.71
3128 3222 0.456824 TCGCTCTGTAGAAGCAAGCG 60.457 55.000 8.63 8.63 44.29 4.68
3222 3321 1.578583 ACCGGAGCATATTTGTACGC 58.421 50.000 9.46 0.00 0.00 4.42
3223 3322 2.286184 GCAACCGGAGCATATTTGTACG 60.286 50.000 9.46 0.00 0.00 3.67
3244 3348 0.578683 CAGCGAACAGTGTGTGACAG 59.421 55.000 0.00 0.00 0.00 3.51
3388 3601 0.530288 AGAGAGACGAGCAAGCTTCC 59.470 55.000 0.00 0.00 0.00 3.46
3447 3660 2.662156 GACTACTGTACTTCGCAGCAAC 59.338 50.000 0.00 0.00 37.47 4.17
3472 3685 6.840780 AAGAAAAATCTCGGTTCATCCAAT 57.159 33.333 0.00 0.00 35.57 3.16
3486 3699 5.048153 ACGCCTAGAAGCAAAGAAAAATC 57.952 39.130 0.00 0.00 0.00 2.17
3487 3700 5.453567 AACGCCTAGAAGCAAAGAAAAAT 57.546 34.783 0.00 0.00 0.00 1.82
3515 3728 0.243636 CGGCAAGACCCCATTTCAAC 59.756 55.000 0.00 0.00 33.26 3.18
3569 3782 4.415332 CACGGACTGACGGACGGG 62.415 72.222 0.00 0.61 38.39 5.28
3572 3785 4.736896 GCCCACGGACTGACGGAC 62.737 72.222 0.00 0.00 38.39 4.79
3576 3789 3.771160 ATCGGCCCACGGACTGAC 61.771 66.667 0.00 0.00 44.45 3.51
3577 3790 3.770040 CATCGGCCCACGGACTGA 61.770 66.667 0.00 0.00 44.45 3.41
3578 3791 4.082523 ACATCGGCCCACGGACTG 62.083 66.667 0.00 0.00 44.45 3.51
3579 3792 4.082523 CACATCGGCCCACGGACT 62.083 66.667 0.00 0.00 44.45 3.85
3580 3793 4.388499 ACACATCGGCCCACGGAC 62.388 66.667 0.00 0.00 44.45 4.79
3581 3794 4.386951 CACACATCGGCCCACGGA 62.387 66.667 0.00 0.00 44.45 4.69
3582 3795 3.303761 TACACACATCGGCCCACGG 62.304 63.158 0.00 0.00 44.45 4.94
3583 3796 2.098233 GTACACACATCGGCCCACG 61.098 63.158 0.00 0.00 46.11 4.94
3584 3797 1.004320 TGTACACACATCGGCCCAC 60.004 57.895 0.00 0.00 0.00 4.61
3585 3798 1.295101 CTGTACACACATCGGCCCA 59.705 57.895 0.00 0.00 33.14 5.36
3586 3799 1.449601 CCTGTACACACATCGGCCC 60.450 63.158 0.00 0.00 33.14 5.80
3587 3800 2.106683 GCCTGTACACACATCGGCC 61.107 63.158 9.80 0.00 39.15 6.13
3588 3801 2.452813 CGCCTGTACACACATCGGC 61.453 63.158 10.69 10.69 40.78 5.54
3589 3802 0.802222 CTCGCCTGTACACACATCGG 60.802 60.000 0.00 0.00 33.78 4.18
3590 3803 0.170339 TCTCGCCTGTACACACATCG 59.830 55.000 0.00 0.00 33.14 3.84
3591 3804 1.469940 CCTCTCGCCTGTACACACATC 60.470 57.143 0.00 0.00 33.14 3.06
3592 3805 0.532573 CCTCTCGCCTGTACACACAT 59.467 55.000 0.00 0.00 33.14 3.21
3593 3806 0.826256 ACCTCTCGCCTGTACACACA 60.826 55.000 0.00 0.00 0.00 3.72
3594 3807 0.388649 CACCTCTCGCCTGTACACAC 60.389 60.000 0.00 0.00 0.00 3.82
3595 3808 1.532604 CCACCTCTCGCCTGTACACA 61.533 60.000 0.00 0.00 0.00 3.72
3596 3809 1.215647 CCACCTCTCGCCTGTACAC 59.784 63.158 0.00 0.00 0.00 2.90
3597 3810 1.076014 TCCACCTCTCGCCTGTACA 59.924 57.895 0.00 0.00 0.00 2.90
3598 3811 1.511768 GTCCACCTCTCGCCTGTAC 59.488 63.158 0.00 0.00 0.00 2.90
3599 3812 2.044555 CGTCCACCTCTCGCCTGTA 61.045 63.158 0.00 0.00 0.00 2.74
3600 3813 3.374402 CGTCCACCTCTCGCCTGT 61.374 66.667 0.00 0.00 0.00 4.00
3601 3814 4.803426 GCGTCCACCTCTCGCCTG 62.803 72.222 0.00 0.00 43.41 4.85
3605 3818 0.526524 GATTCAGCGTCCACCTCTCG 60.527 60.000 0.00 0.00 0.00 4.04
3606 3819 0.820871 AGATTCAGCGTCCACCTCTC 59.179 55.000 0.00 0.00 0.00 3.20
3607 3820 0.534412 CAGATTCAGCGTCCACCTCT 59.466 55.000 0.00 0.00 0.00 3.69
3608 3821 0.532573 TCAGATTCAGCGTCCACCTC 59.467 55.000 0.00 0.00 0.00 3.85
3609 3822 1.137872 GATCAGATTCAGCGTCCACCT 59.862 52.381 0.00 0.00 0.00 4.00
3610 3823 1.134699 TGATCAGATTCAGCGTCCACC 60.135 52.381 0.00 0.00 0.00 4.61
3611 3824 2.200067 CTGATCAGATTCAGCGTCCAC 58.800 52.381 18.34 0.00 36.96 4.02
3612 3825 1.137675 CCTGATCAGATTCAGCGTCCA 59.862 52.381 24.62 0.00 41.50 4.02
3613 3826 1.539929 CCCTGATCAGATTCAGCGTCC 60.540 57.143 24.62 0.00 41.50 4.79
3614 3827 1.410517 TCCCTGATCAGATTCAGCGTC 59.589 52.381 24.62 0.00 41.50 5.19
3615 3828 1.489481 TCCCTGATCAGATTCAGCGT 58.511 50.000 24.62 0.00 41.50 5.07
3616 3829 2.609427 TTCCCTGATCAGATTCAGCG 57.391 50.000 24.62 5.13 41.50 5.18
3617 3830 6.713903 TCAATATTTCCCTGATCAGATTCAGC 59.286 38.462 24.62 0.00 41.50 4.26
3618 3831 7.094720 GCTCAATATTTCCCTGATCAGATTCAG 60.095 40.741 24.62 11.09 42.31 3.02
3619 3832 6.713903 GCTCAATATTTCCCTGATCAGATTCA 59.286 38.462 24.62 5.73 0.00 2.57
3620 3833 6.128336 CGCTCAATATTTCCCTGATCAGATTC 60.128 42.308 24.62 2.71 0.00 2.52
3621 3834 5.704515 CGCTCAATATTTCCCTGATCAGATT 59.295 40.000 24.62 11.34 0.00 2.40
3622 3835 5.012458 TCGCTCAATATTTCCCTGATCAGAT 59.988 40.000 24.62 11.70 0.00 2.90
3623 3836 4.344968 TCGCTCAATATTTCCCTGATCAGA 59.655 41.667 24.62 4.13 0.00 3.27
3624 3837 4.635223 TCGCTCAATATTTCCCTGATCAG 58.365 43.478 16.24 16.24 0.00 2.90
3625 3838 4.635223 CTCGCTCAATATTTCCCTGATCA 58.365 43.478 0.00 0.00 0.00 2.92
3626 3839 3.434984 GCTCGCTCAATATTTCCCTGATC 59.565 47.826 0.00 0.00 0.00 2.92
3627 3840 3.072184 AGCTCGCTCAATATTTCCCTGAT 59.928 43.478 0.00 0.00 0.00 2.90
3628 3841 2.435805 AGCTCGCTCAATATTTCCCTGA 59.564 45.455 0.00 0.00 0.00 3.86
3629 3842 2.547211 CAGCTCGCTCAATATTTCCCTG 59.453 50.000 0.00 0.00 0.00 4.45
3630 3843 2.171448 ACAGCTCGCTCAATATTTCCCT 59.829 45.455 0.00 0.00 0.00 4.20
3631 3844 2.289002 CACAGCTCGCTCAATATTTCCC 59.711 50.000 0.00 0.00 0.00 3.97
3632 3845 2.939103 ACACAGCTCGCTCAATATTTCC 59.061 45.455 0.00 0.00 0.00 3.13
3633 3846 4.142816 ACAACACAGCTCGCTCAATATTTC 60.143 41.667 0.00 0.00 0.00 2.17
3634 3847 3.753272 ACAACACAGCTCGCTCAATATTT 59.247 39.130 0.00 0.00 0.00 1.40
3635 3848 3.338249 ACAACACAGCTCGCTCAATATT 58.662 40.909 0.00 0.00 0.00 1.28
3636 3849 2.932614 GACAACACAGCTCGCTCAATAT 59.067 45.455 0.00 0.00 0.00 1.28
3637 3850 2.029020 AGACAACACAGCTCGCTCAATA 60.029 45.455 0.00 0.00 0.00 1.90
3638 3851 1.151668 GACAACACAGCTCGCTCAAT 58.848 50.000 0.00 0.00 0.00 2.57
3639 3852 0.104855 AGACAACACAGCTCGCTCAA 59.895 50.000 0.00 0.00 0.00 3.02
3640 3853 0.319040 GAGACAACACAGCTCGCTCA 60.319 55.000 0.00 0.00 0.00 4.26
3641 3854 0.038709 AGAGACAACACAGCTCGCTC 60.039 55.000 0.00 0.00 33.98 5.03
3642 3855 0.319383 CAGAGACAACACAGCTCGCT 60.319 55.000 0.00 0.00 33.98 4.93
3643 3856 0.598680 ACAGAGACAACACAGCTCGC 60.599 55.000 0.00 0.00 33.98 5.03
3644 3857 1.524355 CAACAGAGACAACACAGCTCG 59.476 52.381 0.00 0.00 33.98 5.03
3645 3858 2.286294 CACAACAGAGACAACACAGCTC 59.714 50.000 0.00 0.00 0.00 4.09
3646 3859 2.283298 CACAACAGAGACAACACAGCT 58.717 47.619 0.00 0.00 0.00 4.24
3647 3860 1.331756 CCACAACAGAGACAACACAGC 59.668 52.381 0.00 0.00 0.00 4.40
3648 3861 2.868583 CTCCACAACAGAGACAACACAG 59.131 50.000 0.00 0.00 32.86 3.66
3649 3862 2.905075 CTCCACAACAGAGACAACACA 58.095 47.619 0.00 0.00 32.86 3.72
3650 3863 1.599542 GCTCCACAACAGAGACAACAC 59.400 52.381 0.00 0.00 32.86 3.32
3651 3864 1.486310 AGCTCCACAACAGAGACAACA 59.514 47.619 0.00 0.00 32.86 3.33
3652 3865 2.246719 AGCTCCACAACAGAGACAAC 57.753 50.000 0.00 0.00 32.86 3.32
3653 3866 2.945008 CAAAGCTCCACAACAGAGACAA 59.055 45.455 0.00 0.00 32.86 3.18
3654 3867 2.092968 ACAAAGCTCCACAACAGAGACA 60.093 45.455 0.00 0.00 32.86 3.41
3655 3868 2.565841 ACAAAGCTCCACAACAGAGAC 58.434 47.619 0.00 0.00 32.86 3.36
3656 3869 3.281727 AACAAAGCTCCACAACAGAGA 57.718 42.857 0.00 0.00 32.86 3.10
3657 3870 3.243201 GGAAACAAAGCTCCACAACAGAG 60.243 47.826 0.00 0.00 0.00 3.35
3658 3871 2.687935 GGAAACAAAGCTCCACAACAGA 59.312 45.455 0.00 0.00 0.00 3.41
3659 3872 2.223805 GGGAAACAAAGCTCCACAACAG 60.224 50.000 0.00 0.00 32.95 3.16
3660 3873 1.754226 GGGAAACAAAGCTCCACAACA 59.246 47.619 0.00 0.00 32.95 3.33
3661 3874 2.031870 AGGGAAACAAAGCTCCACAAC 58.968 47.619 0.00 0.00 32.95 3.32
3662 3875 2.430332 CAAGGGAAACAAAGCTCCACAA 59.570 45.455 0.00 0.00 32.95 3.33
3663 3876 2.031120 CAAGGGAAACAAAGCTCCACA 58.969 47.619 0.00 0.00 32.95 4.17
3664 3877 1.269778 GCAAGGGAAACAAAGCTCCAC 60.270 52.381 0.00 0.00 32.95 4.02
3665 3878 1.039856 GCAAGGGAAACAAAGCTCCA 58.960 50.000 0.00 0.00 32.95 3.86
3666 3879 1.039856 TGCAAGGGAAACAAAGCTCC 58.960 50.000 0.00 0.00 0.00 4.70
3667 3880 4.519540 TTATGCAAGGGAAACAAAGCTC 57.480 40.909 0.00 0.00 0.00 4.09
3668 3881 5.488262 AATTATGCAAGGGAAACAAAGCT 57.512 34.783 0.00 0.00 0.00 3.74
3669 3882 5.700373 TGAAATTATGCAAGGGAAACAAAGC 59.300 36.000 0.00 0.00 0.00 3.51
3670 3883 7.910441 ATGAAATTATGCAAGGGAAACAAAG 57.090 32.000 0.00 0.00 0.00 2.77
3671 3884 8.592809 AGTATGAAATTATGCAAGGGAAACAAA 58.407 29.630 0.00 0.00 0.00 2.83
3672 3885 8.133024 AGTATGAAATTATGCAAGGGAAACAA 57.867 30.769 0.00 0.00 0.00 2.83
3673 3886 7.716799 AGTATGAAATTATGCAAGGGAAACA 57.283 32.000 0.00 0.00 0.00 2.83
3674 3887 7.855904 CGTAGTATGAAATTATGCAAGGGAAAC 59.144 37.037 0.00 0.00 0.00 2.78
3675 3888 7.554835 ACGTAGTATGAAATTATGCAAGGGAAA 59.445 33.333 0.00 0.00 41.94 3.13
3676 3889 7.051623 ACGTAGTATGAAATTATGCAAGGGAA 58.948 34.615 0.00 0.00 41.94 3.97
3677 3890 6.588204 ACGTAGTATGAAATTATGCAAGGGA 58.412 36.000 0.00 0.00 41.94 4.20
3678 3891 6.861065 ACGTAGTATGAAATTATGCAAGGG 57.139 37.500 0.00 0.00 41.94 3.95
3700 3913 5.005779 ACATACTGTAGTACGTACGCAGTAC 59.994 44.000 37.82 27.60 45.00 2.73
3701 3914 5.109210 ACATACTGTAGTACGTACGCAGTA 58.891 41.667 37.47 37.47 44.66 2.74
3702 3915 3.935203 ACATACTGTAGTACGTACGCAGT 59.065 43.478 36.47 36.47 43.73 4.40
3703 3916 4.526970 ACATACTGTAGTACGTACGCAG 57.473 45.455 32.17 32.17 38.79 5.18
3704 3917 4.201812 GGAACATACTGTAGTACGTACGCA 60.202 45.833 19.49 19.50 33.87 5.24
3705 3918 4.201812 TGGAACATACTGTAGTACGTACGC 60.202 45.833 19.49 16.28 33.87 4.42
3706 3919 5.291858 TCTGGAACATACTGTAGTACGTACG 59.708 44.000 19.49 15.01 38.20 3.67
3707 3920 6.668541 TCTGGAACATACTGTAGTACGTAC 57.331 41.667 18.10 18.10 38.20 3.67
3708 3921 8.996271 CATATCTGGAACATACTGTAGTACGTA 58.004 37.037 0.00 0.00 38.20 3.57
3709 3922 7.718314 TCATATCTGGAACATACTGTAGTACGT 59.282 37.037 0.00 0.00 38.20 3.57
3710 3923 8.095937 TCATATCTGGAACATACTGTAGTACG 57.904 38.462 0.00 0.00 38.20 3.67
3713 3926 9.988815 GAAATCATATCTGGAACATACTGTAGT 57.011 33.333 0.00 0.00 38.20 2.73
3714 3927 9.133627 CGAAATCATATCTGGAACATACTGTAG 57.866 37.037 0.00 0.00 38.20 2.74
3715 3928 7.598869 GCGAAATCATATCTGGAACATACTGTA 59.401 37.037 0.00 0.00 38.20 2.74
3716 3929 6.425114 GCGAAATCATATCTGGAACATACTGT 59.575 38.462 0.00 0.00 38.20 3.55
3717 3930 6.128445 GGCGAAATCATATCTGGAACATACTG 60.128 42.308 0.00 0.00 38.20 2.74
3718 3931 5.934625 GGCGAAATCATATCTGGAACATACT 59.065 40.000 0.00 0.00 38.20 2.12
3719 3932 5.163953 CGGCGAAATCATATCTGGAACATAC 60.164 44.000 0.00 0.00 38.20 2.39
3720 3933 4.929211 CGGCGAAATCATATCTGGAACATA 59.071 41.667 0.00 0.00 38.20 2.29
3721 3934 3.748048 CGGCGAAATCATATCTGGAACAT 59.252 43.478 0.00 0.00 38.20 2.71
3722 3935 3.130633 CGGCGAAATCATATCTGGAACA 58.869 45.455 0.00 0.00 0.00 3.18
3723 3936 2.096218 GCGGCGAAATCATATCTGGAAC 60.096 50.000 12.98 0.00 0.00 3.62
3724 3937 2.143122 GCGGCGAAATCATATCTGGAA 58.857 47.619 12.98 0.00 0.00 3.53
3725 3938 1.069978 TGCGGCGAAATCATATCTGGA 59.930 47.619 12.98 0.00 0.00 3.86
3726 3939 1.511850 TGCGGCGAAATCATATCTGG 58.488 50.000 12.98 0.00 0.00 3.86
3727 3940 2.096069 CCTTGCGGCGAAATCATATCTG 60.096 50.000 12.98 0.00 0.00 2.90
3728 3941 2.146342 CCTTGCGGCGAAATCATATCT 58.854 47.619 12.98 0.00 0.00 1.98
3729 3942 2.143122 TCCTTGCGGCGAAATCATATC 58.857 47.619 12.98 0.00 0.00 1.63
3730 3943 2.254546 TCCTTGCGGCGAAATCATAT 57.745 45.000 12.98 0.00 0.00 1.78
3731 3944 1.668751 GTTCCTTGCGGCGAAATCATA 59.331 47.619 12.98 0.00 0.00 2.15
3732 3945 0.451783 GTTCCTTGCGGCGAAATCAT 59.548 50.000 12.98 0.00 0.00 2.45
3733 3946 0.886938 TGTTCCTTGCGGCGAAATCA 60.887 50.000 12.98 0.69 0.00 2.57
3734 3947 0.179189 CTGTTCCTTGCGGCGAAATC 60.179 55.000 12.98 0.00 0.00 2.17
3735 3948 1.875963 CTGTTCCTTGCGGCGAAAT 59.124 52.632 12.98 0.00 0.00 2.17
3736 3949 2.903547 GCTGTTCCTTGCGGCGAAA 61.904 57.895 12.98 5.23 0.00 3.46
3737 3950 3.353836 GCTGTTCCTTGCGGCGAA 61.354 61.111 12.98 0.00 0.00 4.70
3740 3953 3.741476 CAGGCTGTTCCTTGCGGC 61.741 66.667 6.28 0.00 44.75 6.53
3741 3954 3.058160 CCAGGCTGTTCCTTGCGG 61.058 66.667 14.43 0.00 44.75 5.69
3742 3955 2.281761 ACCAGGCTGTTCCTTGCG 60.282 61.111 14.43 0.00 44.75 4.85
3743 3956 1.228245 TCACCAGGCTGTTCCTTGC 60.228 57.895 14.43 0.00 44.75 4.01
3744 3957 0.109342 ACTCACCAGGCTGTTCCTTG 59.891 55.000 14.43 0.00 44.75 3.61
3745 3958 0.846693 AACTCACCAGGCTGTTCCTT 59.153 50.000 14.43 0.00 44.75 3.36
3747 3960 0.951040 CGAACTCACCAGGCTGTTCC 60.951 60.000 14.43 0.00 36.43 3.62
3748 3961 0.033504 TCGAACTCACCAGGCTGTTC 59.966 55.000 14.43 9.07 36.44 3.18
3749 3962 0.468226 TTCGAACTCACCAGGCTGTT 59.532 50.000 14.43 0.00 0.00 3.16
3750 3963 0.034059 CTTCGAACTCACCAGGCTGT 59.966 55.000 14.43 0.00 0.00 4.40
3751 3964 1.294659 GCTTCGAACTCACCAGGCTG 61.295 60.000 7.75 7.75 0.00 4.85
3752 3965 1.004440 GCTTCGAACTCACCAGGCT 60.004 57.895 0.00 0.00 0.00 4.58
3753 3966 2.383527 CGCTTCGAACTCACCAGGC 61.384 63.158 0.00 0.00 0.00 4.85
3754 3967 0.242825 TACGCTTCGAACTCACCAGG 59.757 55.000 0.00 0.00 0.00 4.45
3755 3968 1.068472 ACTACGCTTCGAACTCACCAG 60.068 52.381 0.00 0.00 0.00 4.00
3756 3969 0.956633 ACTACGCTTCGAACTCACCA 59.043 50.000 0.00 0.00 0.00 4.17
3757 3970 1.615502 GACTACGCTTCGAACTCACC 58.384 55.000 0.00 0.00 0.00 4.02
3758 3971 1.248721 CGACTACGCTTCGAACTCAC 58.751 55.000 0.00 0.00 38.85 3.51
3759 3972 0.870393 ACGACTACGCTTCGAACTCA 59.130 50.000 7.80 0.00 43.96 3.41
3760 3973 1.248721 CACGACTACGCTTCGAACTC 58.751 55.000 7.80 0.00 43.96 3.01
3761 3974 0.109873 CCACGACTACGCTTCGAACT 60.110 55.000 7.80 0.00 43.96 3.01
3762 3975 0.110056 TCCACGACTACGCTTCGAAC 60.110 55.000 7.80 0.00 43.96 3.95
3763 3976 0.806868 ATCCACGACTACGCTTCGAA 59.193 50.000 7.80 0.00 43.96 3.71
3764 3977 0.098200 CATCCACGACTACGCTTCGA 59.902 55.000 7.80 0.00 43.96 3.71
3765 3978 1.472276 GCATCCACGACTACGCTTCG 61.472 60.000 0.00 0.00 43.96 3.79
3766 3979 0.457853 TGCATCCACGACTACGCTTC 60.458 55.000 0.00 0.00 43.96 3.86
3767 3980 0.736325 GTGCATCCACGACTACGCTT 60.736 55.000 0.00 0.00 43.96 4.68
3768 3981 1.153823 GTGCATCCACGACTACGCT 60.154 57.895 0.00 0.00 43.96 5.07
3769 3982 2.165301 GGTGCATCCACGACTACGC 61.165 63.158 0.00 0.00 43.00 4.42
3770 3983 4.088421 GGTGCATCCACGACTACG 57.912 61.111 0.00 0.00 43.00 3.51


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

AutoCloner maintained by Alex Coulton.