Multiple sequence alignment - TraesCS6A01G090300

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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 TraesCS6A01G090300 chr6A 100.000 4308 0 0 1 4308 58147514 58151821 0.000000e+00 7956.0
1 TraesCS6A01G090300 chr6A 92.971 754 40 6 40 782 93167331 93168082 0.000000e+00 1086.0
2 TraesCS6A01G090300 chr6B 90.936 2041 95 33 1771 3761 93998544 94000544 0.000000e+00 2662.0
3 TraesCS6A01G090300 chr6B 93.808 969 27 11 818 1778 93997565 93998508 0.000000e+00 1426.0
4 TraesCS6A01G090300 chr6D 90.581 1412 71 23 2385 3761 42565253 42563869 0.000000e+00 1814.0
5 TraesCS6A01G090300 chr6D 95.963 966 22 7 825 1778 42566985 42566025 0.000000e+00 1552.0
6 TraesCS6A01G090300 chr6D 96.066 610 24 0 1777 2386 42565984 42565375 0.000000e+00 994.0
7 TraesCS6A01G090300 chr6D 85.127 511 22 26 3841 4308 42563904 42563405 1.400000e-129 473.0
8 TraesCS6A01G090300 chr6D 100.000 28 0 0 1055 1082 243691737 243691710 8.000000e-03 52.8
9 TraesCS6A01G090300 chr3B 96.366 798 16 5 1 794 74727126 74727914 0.000000e+00 1301.0
10 TraesCS6A01G090300 chr7B 93.585 795 44 6 1 793 679530696 679529907 0.000000e+00 1179.0
11 TraesCS6A01G090300 chr1B 92.358 759 51 5 40 793 667908102 667908858 0.000000e+00 1074.0
12 TraesCS6A01G090300 chr5A 91.310 771 46 9 43 794 166541395 166540627 0.000000e+00 1033.0
13 TraesCS6A01G090300 chr5A 90.427 773 48 9 40 793 379035906 379036671 0.000000e+00 994.0
14 TraesCS6A01G090300 chr5A 90.369 758 66 6 40 793 420392560 420391806 0.000000e+00 989.0
15 TraesCS6A01G090300 chr7A 90.921 760 60 7 40 794 6780201 6779446 0.000000e+00 1013.0
16 TraesCS6A01G090300 chr2B 90.395 760 58 10 40 794 363635516 363636265 0.000000e+00 985.0
17 TraesCS6A01G090300 chr3A 94.397 232 11 2 40 270 365958569 365958339 5.300000e-94 355.0
18 TraesCS6A01G090300 chr5D 100.000 32 0 0 1051 1082 16010386 16010417 4.650000e-05 60.2
19 TraesCS6A01G090300 chr5D 96.875 32 1 0 1051 1082 164104116 164104085 2.000000e-03 54.7
20 TraesCS6A01G090300 chr4D 100.000 32 0 0 1051 1082 59706678 59706709 4.650000e-05 60.2
21 TraesCS6A01G090300 chr2D 100.000 32 0 0 1051 1082 632278578 632278609 4.650000e-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 TraesCS6A01G090300 chr6A 58147514 58151821 4307 False 7956.00 7956 100.00000 1 4308 1 chr6A.!!$F1 4307
1 TraesCS6A01G090300 chr6A 93167331 93168082 751 False 1086.00 1086 92.97100 40 782 1 chr6A.!!$F2 742
2 TraesCS6A01G090300 chr6B 93997565 94000544 2979 False 2044.00 2662 92.37200 818 3761 2 chr6B.!!$F1 2943
3 TraesCS6A01G090300 chr6D 42563405 42566985 3580 True 1208.25 1814 91.93425 825 4308 4 chr6D.!!$R2 3483
4 TraesCS6A01G090300 chr3B 74727126 74727914 788 False 1301.00 1301 96.36600 1 794 1 chr3B.!!$F1 793
5 TraesCS6A01G090300 chr7B 679529907 679530696 789 True 1179.00 1179 93.58500 1 793 1 chr7B.!!$R1 792
6 TraesCS6A01G090300 chr1B 667908102 667908858 756 False 1074.00 1074 92.35800 40 793 1 chr1B.!!$F1 753
7 TraesCS6A01G090300 chr5A 166540627 166541395 768 True 1033.00 1033 91.31000 43 794 1 chr5A.!!$R1 751
8 TraesCS6A01G090300 chr5A 379035906 379036671 765 False 994.00 994 90.42700 40 793 1 chr5A.!!$F1 753
9 TraesCS6A01G090300 chr5A 420391806 420392560 754 True 989.00 989 90.36900 40 793 1 chr5A.!!$R2 753
10 TraesCS6A01G090300 chr7A 6779446 6780201 755 True 1013.00 1013 90.92100 40 794 1 chr7A.!!$R1 754
11 TraesCS6A01G090300 chr2B 363635516 363636265 749 False 985.00 985 90.39500 40 794 1 chr2B.!!$F1 754

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
814 841 0.320697 AGAAGAACCGGGTAGCACAC 59.679 55.000 6.32 0.0 0.00 3.82 F
930 958 0.924226 TTTCCCCCATCCTTCCTCCC 60.924 60.000 0.00 0.0 0.00 4.30 F
937 965 1.075151 ATCCTTCCTCCCTCGTCCC 60.075 63.158 0.00 0.0 0.00 4.46 F
2302 2396 0.749649 ACCTTGCCGCACAATTTCAA 59.250 45.000 0.00 0.0 37.72 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1773 1.002033 CTAAGCGCTTCCATCCATTGC 60.002 52.381 28.82 0.0 0.00 3.56 R
1987 2081 1.478510 CTAGTGACCTCGCTGGATGTT 59.521 52.381 0.00 0.0 37.16 2.71 R
2787 3008 1.750206 TCAACAGCAACAGCAACATGT 59.250 42.857 0.00 0.0 33.96 3.21 R
3803 4094 0.030908 CTGAAGGTCCTATCCGACGC 59.969 60.000 0.00 0.0 33.30 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
162 171 1.056660 AACCTCAACGGGTGATGTCT 58.943 50.000 4.41 0.00 39.85 3.41
303 314 7.506261 ATCAGTAGGATAACCACGAGAGTATTT 59.494 37.037 0.00 0.00 36.86 1.40
776 803 4.265904 ACCAAATTTTAAGAAAGGGCCG 57.734 40.909 0.00 0.00 0.00 6.13
794 821 4.061596 GGCCGAATAAGGAATTCTCTCAG 58.938 47.826 5.23 0.00 41.68 3.35
795 822 4.202264 GGCCGAATAAGGAATTCTCTCAGA 60.202 45.833 5.23 0.00 41.68 3.27
796 823 4.987912 GCCGAATAAGGAATTCTCTCAGAG 59.012 45.833 5.23 0.00 41.68 3.35
797 824 5.221342 GCCGAATAAGGAATTCTCTCAGAGA 60.221 44.000 0.00 0.00 41.68 3.10
806 833 1.840737 TCTCTCAGAGAAGAACCGGG 58.159 55.000 6.32 0.00 35.59 5.73
807 834 1.075698 TCTCTCAGAGAAGAACCGGGT 59.924 52.381 6.32 0.00 35.59 5.28
808 835 2.307980 TCTCTCAGAGAAGAACCGGGTA 59.692 50.000 6.32 0.00 35.59 3.69
809 836 2.685897 CTCTCAGAGAAGAACCGGGTAG 59.314 54.545 6.32 0.00 0.00 3.18
810 837 1.135333 CTCAGAGAAGAACCGGGTAGC 59.865 57.143 6.32 0.00 0.00 3.58
811 838 0.895530 CAGAGAAGAACCGGGTAGCA 59.104 55.000 6.32 0.00 0.00 3.49
812 839 0.896226 AGAGAAGAACCGGGTAGCAC 59.104 55.000 6.32 0.00 0.00 4.40
813 840 0.606604 GAGAAGAACCGGGTAGCACA 59.393 55.000 6.32 0.00 0.00 4.57
814 841 0.320697 AGAAGAACCGGGTAGCACAC 59.679 55.000 6.32 0.00 0.00 3.82
879 907 4.725556 TTCCGAATCTCAAAGACAAACG 57.274 40.909 0.00 0.00 0.00 3.60
929 957 1.007607 TTTTCCCCCATCCTTCCTCC 58.992 55.000 0.00 0.00 0.00 4.30
930 958 0.924226 TTTCCCCCATCCTTCCTCCC 60.924 60.000 0.00 0.00 0.00 4.30
931 959 1.848835 TTCCCCCATCCTTCCTCCCT 61.849 60.000 0.00 0.00 0.00 4.20
932 960 1.772156 CCCCCATCCTTCCTCCCTC 60.772 68.421 0.00 0.00 0.00 4.30
933 961 2.143419 CCCCATCCTTCCTCCCTCG 61.143 68.421 0.00 0.00 0.00 4.63
934 962 1.383248 CCCATCCTTCCTCCCTCGT 60.383 63.158 0.00 0.00 0.00 4.18
935 963 1.403687 CCCATCCTTCCTCCCTCGTC 61.404 65.000 0.00 0.00 0.00 4.20
936 964 1.403687 CCATCCTTCCTCCCTCGTCC 61.404 65.000 0.00 0.00 0.00 4.79
937 965 1.075151 ATCCTTCCTCCCTCGTCCC 60.075 63.158 0.00 0.00 0.00 4.46
938 966 2.607139 ATCCTTCCTCCCTCGTCCCC 62.607 65.000 0.00 0.00 0.00 4.81
1101 1139 4.773117 GTGGAGGCCGTCGTCGTC 62.773 72.222 0.00 0.00 35.01 4.20
1245 1283 3.692406 GAGTCCGCCGACCAGGTT 61.692 66.667 0.00 0.00 43.70 3.50
1255 1293 1.229723 GACCAGGTTACCTCCCCCA 60.230 63.158 0.00 0.00 0.00 4.96
1263 1301 2.820899 TTACCTCCCCCACCCCGTAC 62.821 65.000 0.00 0.00 0.00 3.67
1289 1327 2.482326 CCCGAAGCTGGGCTAAAAG 58.518 57.895 0.00 0.00 43.70 2.27
1362 1400 4.281898 TCTAGGGTTTGTTAGTTGAGCC 57.718 45.455 0.00 0.00 0.00 4.70
1618 1664 3.133691 CCATGTGCGCATAGACAGTTAT 58.866 45.455 15.91 0.00 33.30 1.89
1619 1665 3.561310 CCATGTGCGCATAGACAGTTATT 59.439 43.478 15.91 0.00 33.30 1.40
1620 1666 4.521010 CATGTGCGCATAGACAGTTATTG 58.479 43.478 15.91 0.00 33.30 1.90
1724 1773 3.569701 AGCACCTGTCACTGTAATTTTGG 59.430 43.478 0.00 0.00 0.00 3.28
1741 1790 2.123428 GGCAATGGATGGAAGCGCT 61.123 57.895 2.64 2.64 0.00 5.92
1825 1917 7.140705 TGATAACACAAATTGACTTGAGCTTG 58.859 34.615 0.00 0.00 0.00 4.01
1836 1930 6.036577 TGACTTGAGCTTGTACATATGACA 57.963 37.500 10.38 6.80 0.00 3.58
1866 1960 5.767665 TGTATTTGTGTTTGCATAGACACCT 59.232 36.000 19.50 8.73 44.18 4.00
1867 1961 4.829064 TTTGTGTTTGCATAGACACCTC 57.171 40.909 19.50 3.16 44.18 3.85
1944 2038 4.607293 TCATGTTCTGTCTAGTGCTGTT 57.393 40.909 0.00 0.00 0.00 3.16
1954 2048 2.226674 TCTAGTGCTGTTGACAGAGTCG 59.773 50.000 14.98 0.00 46.59 4.18
1965 2059 2.826128 TGACAGAGTCGCTCTAACCAAT 59.174 45.455 8.70 0.00 38.99 3.16
1987 2081 4.917385 TGATTAAGGGTAGCAGCAAAAGA 58.083 39.130 0.00 0.00 0.00 2.52
2302 2396 0.749649 ACCTTGCCGCACAATTTCAA 59.250 45.000 0.00 0.00 37.72 2.69
2417 2634 5.265191 TCTACTCTGTTGATCTGGTAGCTT 58.735 41.667 0.00 0.00 0.00 3.74
2505 2722 6.741992 TGCACTGAACTAAATGAGGTATTG 57.258 37.500 0.00 0.00 0.00 1.90
2538 2756 3.318839 TGAGCAACAAAAACCTGATGAGG 59.681 43.478 0.00 0.00 46.21 3.86
2576 2797 9.019656 TCTGCCAGTAAATTTGAAAATAGCTTA 57.980 29.630 0.00 0.00 0.00 3.09
2577 2798 9.807649 CTGCCAGTAAATTTGAAAATAGCTTAT 57.192 29.630 0.00 0.00 0.00 1.73
2578 2799 9.585099 TGCCAGTAAATTTGAAAATAGCTTATG 57.415 29.630 0.00 0.00 0.00 1.90
2579 2800 8.542953 GCCAGTAAATTTGAAAATAGCTTATGC 58.457 33.333 0.00 0.00 40.05 3.14
2615 2836 9.581099 CTTCTGTTTTTGTGTAAAAATAGTGGT 57.419 29.630 16.24 0.00 40.33 4.16
2660 2881 8.255111 AGGATTCTTTGTTCTTGGAAGAAAAT 57.745 30.769 3.38 0.52 45.77 1.82
2832 3058 6.488006 ACACAGTTGAAATGCTGAAATCTACT 59.512 34.615 0.00 0.00 36.62 2.57
2887 3113 5.279156 GGAATGGAGTCTTCAATGCAAAAGT 60.279 40.000 0.00 0.00 0.00 2.66
2958 3184 2.242043 AGAAATTGTCCTGCCACTTGG 58.758 47.619 0.00 0.00 38.53 3.61
3179 3408 6.483307 TGATAAATGGCTATCTTGGTTTCTCG 59.517 38.462 0.00 0.00 30.80 4.04
3271 3500 1.450848 ACGGACTCAGATCGCGGTA 60.451 57.895 6.13 0.00 0.00 4.02
3345 3576 2.360350 CTGCCAACTCCATGCCGT 60.360 61.111 0.00 0.00 0.00 5.68
3346 3577 2.672651 TGCCAACTCCATGCCGTG 60.673 61.111 0.00 0.00 0.00 4.94
3347 3578 2.359850 GCCAACTCCATGCCGTGA 60.360 61.111 0.00 0.00 0.00 4.35
3348 3579 2.690778 GCCAACTCCATGCCGTGAC 61.691 63.158 0.00 0.00 0.00 3.67
3349 3580 1.302431 CCAACTCCATGCCGTGACA 60.302 57.895 0.00 0.00 0.00 3.58
3350 3581 1.300971 CCAACTCCATGCCGTGACAG 61.301 60.000 0.00 0.00 0.00 3.51
3351 3582 1.672356 AACTCCATGCCGTGACAGC 60.672 57.895 0.00 0.00 0.00 4.40
3352 3583 2.046988 CTCCATGCCGTGACAGCA 60.047 61.111 0.00 0.00 45.94 4.41
3476 3728 1.993956 TGTTTGCACTAATGTGGGCT 58.006 45.000 0.00 0.00 43.97 5.19
3502 3760 8.336235 TCAGACCTTTCCATTGGATTTAGTATT 58.664 33.333 6.15 0.00 0.00 1.89
3534 3792 8.121305 TGTTTCTGGCTGAATATTTGTAATGT 57.879 30.769 7.68 0.00 34.24 2.71
3554 3835 6.655078 ATGTCTGATACTGGCTTTGTTTTT 57.345 33.333 0.00 0.00 0.00 1.94
3555 3836 6.072112 TGTCTGATACTGGCTTTGTTTTTC 57.928 37.500 0.00 0.00 0.00 2.29
3557 3838 6.321181 TGTCTGATACTGGCTTTGTTTTTCTT 59.679 34.615 0.00 0.00 0.00 2.52
3559 3840 5.841810 TGATACTGGCTTTGTTTTTCTTGG 58.158 37.500 0.00 0.00 0.00 3.61
3561 3842 4.551702 ACTGGCTTTGTTTTTCTTGGTT 57.448 36.364 0.00 0.00 0.00 3.67
3563 3844 4.222810 ACTGGCTTTGTTTTTCTTGGTTCT 59.777 37.500 0.00 0.00 0.00 3.01
3564 3845 4.754322 TGGCTTTGTTTTTCTTGGTTCTC 58.246 39.130 0.00 0.00 0.00 2.87
3568 3849 6.036083 GGCTTTGTTTTTCTTGGTTCTCTTTC 59.964 38.462 0.00 0.00 0.00 2.62
3693 3984 3.858238 GTGTTGTACGGAAGAGTCTATGC 59.142 47.826 0.00 0.00 0.00 3.14
3701 3992 3.682718 CGGAAGAGTCTATGCCAAATGGT 60.683 47.826 0.71 0.00 37.57 3.55
3750 4041 6.408662 GGAAGCTATAGAGATCAAACCCTTGT 60.409 42.308 3.21 0.00 33.94 3.16
3761 4052 0.178953 AACCCTTGTGGCAGAGCATT 60.179 50.000 0.00 0.00 37.83 3.56
3762 4053 0.896940 ACCCTTGTGGCAGAGCATTG 60.897 55.000 0.00 0.00 37.83 2.82
3763 4054 1.214589 CCTTGTGGCAGAGCATTGC 59.785 57.895 0.00 0.00 43.34 3.56
3764 4055 1.154093 CTTGTGGCAGAGCATTGCG 60.154 57.895 2.38 0.00 45.00 4.85
3765 4056 2.537792 CTTGTGGCAGAGCATTGCGG 62.538 60.000 2.38 0.00 45.00 5.69
3766 4057 3.058160 GTGGCAGAGCATTGCGGT 61.058 61.111 2.38 0.00 45.00 5.68
3767 4058 3.057548 TGGCAGAGCATTGCGGTG 61.058 61.111 2.38 5.99 45.00 4.94
3768 4059 3.818787 GGCAGAGCATTGCGGTGG 61.819 66.667 13.15 2.80 45.00 4.61
3769 4060 4.487412 GCAGAGCATTGCGGTGGC 62.487 66.667 13.15 8.18 40.52 5.01
3770 4061 2.749044 CAGAGCATTGCGGTGGCT 60.749 61.111 2.38 0.00 41.35 4.75
3771 4062 2.749044 AGAGCATTGCGGTGGCTG 60.749 61.111 2.38 0.00 38.15 4.85
3772 4063 3.818787 GAGCATTGCGGTGGCTGG 61.819 66.667 2.38 0.00 38.15 4.85
3773 4064 4.666253 AGCATTGCGGTGGCTGGT 62.666 61.111 2.38 0.00 40.82 4.00
3774 4065 4.424566 GCATTGCGGTGGCTGGTG 62.425 66.667 0.00 0.00 40.82 4.17
3775 4066 2.985282 CATTGCGGTGGCTGGTGT 60.985 61.111 0.00 0.00 40.82 4.16
3776 4067 1.673993 CATTGCGGTGGCTGGTGTA 60.674 57.895 0.00 0.00 40.82 2.90
3777 4068 1.674322 ATTGCGGTGGCTGGTGTAC 60.674 57.895 0.00 0.00 40.82 2.90
3778 4069 2.404566 ATTGCGGTGGCTGGTGTACA 62.405 55.000 0.00 0.00 40.82 2.90
3779 4070 2.046314 GCGGTGGCTGGTGTACAT 60.046 61.111 0.00 0.00 35.83 2.29
3780 4071 2.398554 GCGGTGGCTGGTGTACATG 61.399 63.158 0.00 0.00 35.83 3.21
3781 4072 1.295101 CGGTGGCTGGTGTACATGA 59.705 57.895 0.00 0.00 0.00 3.07
3782 4073 0.321210 CGGTGGCTGGTGTACATGAA 60.321 55.000 0.00 0.00 0.00 2.57
3783 4074 1.453155 GGTGGCTGGTGTACATGAAG 58.547 55.000 0.00 0.00 0.00 3.02
3784 4075 1.003118 GGTGGCTGGTGTACATGAAGA 59.997 52.381 0.00 0.00 0.00 2.87
3785 4076 2.356125 GGTGGCTGGTGTACATGAAGAT 60.356 50.000 0.00 0.00 0.00 2.40
3786 4077 2.679837 GTGGCTGGTGTACATGAAGATG 59.320 50.000 0.00 0.00 35.49 2.90
3787 4078 2.571202 TGGCTGGTGTACATGAAGATGA 59.429 45.455 0.00 0.00 33.36 2.92
3788 4079 3.201290 GGCTGGTGTACATGAAGATGAG 58.799 50.000 0.00 0.00 33.36 2.90
3789 4080 3.201290 GCTGGTGTACATGAAGATGAGG 58.799 50.000 0.00 0.00 33.36 3.86
3790 4081 3.369892 GCTGGTGTACATGAAGATGAGGT 60.370 47.826 0.00 0.00 33.36 3.85
3791 4082 4.836825 CTGGTGTACATGAAGATGAGGTT 58.163 43.478 0.00 0.00 33.36 3.50
3792 4083 4.578871 TGGTGTACATGAAGATGAGGTTG 58.421 43.478 0.00 0.00 33.36 3.77
3793 4084 4.285775 TGGTGTACATGAAGATGAGGTTGA 59.714 41.667 0.00 0.00 33.36 3.18
3794 4085 5.221823 TGGTGTACATGAAGATGAGGTTGAA 60.222 40.000 0.00 0.00 33.36 2.69
3795 4086 5.352569 GGTGTACATGAAGATGAGGTTGAAG 59.647 44.000 0.00 0.00 33.36 3.02
3796 4087 4.937620 TGTACATGAAGATGAGGTTGAAGC 59.062 41.667 0.00 0.00 33.36 3.86
3797 4088 4.298103 ACATGAAGATGAGGTTGAAGCT 57.702 40.909 0.00 0.00 33.36 3.74
3798 4089 4.660168 ACATGAAGATGAGGTTGAAGCTT 58.340 39.130 0.00 0.00 33.36 3.74
3799 4090 5.809001 ACATGAAGATGAGGTTGAAGCTTA 58.191 37.500 0.00 0.00 33.36 3.09
3800 4091 5.879223 ACATGAAGATGAGGTTGAAGCTTAG 59.121 40.000 0.00 0.00 33.36 2.18
3801 4092 4.836825 TGAAGATGAGGTTGAAGCTTAGG 58.163 43.478 0.00 0.00 0.00 2.69
3802 4093 3.922171 AGATGAGGTTGAAGCTTAGGG 57.078 47.619 0.00 0.00 0.00 3.53
3803 4094 2.507471 AGATGAGGTTGAAGCTTAGGGG 59.493 50.000 0.00 0.00 0.00 4.79
3804 4095 0.328258 TGAGGTTGAAGCTTAGGGGC 59.672 55.000 0.00 0.00 0.00 5.80
3805 4096 0.744771 GAGGTTGAAGCTTAGGGGCG 60.745 60.000 0.00 0.00 37.29 6.13
3806 4097 1.002502 GGTTGAAGCTTAGGGGCGT 60.003 57.895 0.00 0.00 37.29 5.68
3807 4098 1.025113 GGTTGAAGCTTAGGGGCGTC 61.025 60.000 0.00 0.00 40.21 5.19
3808 4099 1.079405 TTGAAGCTTAGGGGCGTCG 60.079 57.895 0.00 0.00 42.08 5.12
3809 4100 2.202892 GAAGCTTAGGGGCGTCGG 60.203 66.667 0.00 0.00 37.29 4.79
3810 4101 2.682494 AAGCTTAGGGGCGTCGGA 60.682 61.111 0.00 0.00 37.29 4.55
3811 4102 2.029307 GAAGCTTAGGGGCGTCGGAT 62.029 60.000 0.00 0.00 37.29 4.18
3812 4103 0.757935 AAGCTTAGGGGCGTCGGATA 60.758 55.000 0.00 0.00 37.29 2.59
3813 4104 1.179814 AGCTTAGGGGCGTCGGATAG 61.180 60.000 0.00 0.00 37.29 2.08
3814 4105 1.965219 CTTAGGGGCGTCGGATAGG 59.035 63.158 0.00 0.00 0.00 2.57
3815 4106 0.538977 CTTAGGGGCGTCGGATAGGA 60.539 60.000 0.00 0.00 0.00 2.94
3816 4107 0.825010 TTAGGGGCGTCGGATAGGAC 60.825 60.000 0.00 0.00 0.00 3.85
3817 4108 2.703675 TAGGGGCGTCGGATAGGACC 62.704 65.000 0.00 0.00 40.78 4.46
3818 4109 2.521224 GGGCGTCGGATAGGACCT 60.521 66.667 0.00 0.00 38.22 3.85
3819 4110 2.132352 GGGCGTCGGATAGGACCTT 61.132 63.158 0.00 0.00 38.22 3.50
3820 4111 1.363080 GGCGTCGGATAGGACCTTC 59.637 63.158 0.00 0.00 33.30 3.46
3821 4112 1.389609 GGCGTCGGATAGGACCTTCA 61.390 60.000 0.00 0.00 33.30 3.02
3822 4113 0.030908 GCGTCGGATAGGACCTTCAG 59.969 60.000 0.00 0.00 33.30 3.02
3823 4114 1.676746 CGTCGGATAGGACCTTCAGA 58.323 55.000 0.00 0.97 33.30 3.27
3824 4115 1.604755 CGTCGGATAGGACCTTCAGAG 59.395 57.143 0.00 0.00 33.30 3.35
3826 4117 1.850998 TCGGATAGGACCTTCAGAGGA 59.149 52.381 0.00 0.00 46.74 3.71
3827 4118 1.957877 CGGATAGGACCTTCAGAGGAC 59.042 57.143 0.00 0.00 46.74 3.85
3828 4119 2.687014 CGGATAGGACCTTCAGAGGACA 60.687 54.545 0.00 0.00 46.74 4.02
3829 4120 2.962421 GGATAGGACCTTCAGAGGACAG 59.038 54.545 0.00 0.00 46.74 3.51
3830 4121 2.534042 TAGGACCTTCAGAGGACAGG 57.466 55.000 0.00 0.00 46.74 4.00
3831 4122 0.489567 AGGACCTTCAGAGGACAGGT 59.510 55.000 0.00 0.00 46.74 4.00
3832 4123 1.132689 AGGACCTTCAGAGGACAGGTT 60.133 52.381 0.00 0.00 46.74 3.50
3833 4124 1.002544 GGACCTTCAGAGGACAGGTTG 59.997 57.143 0.00 0.00 46.74 3.77
3834 4125 1.971357 GACCTTCAGAGGACAGGTTGA 59.029 52.381 0.00 0.00 46.74 3.18
3835 4126 2.368875 GACCTTCAGAGGACAGGTTGAA 59.631 50.000 0.00 0.00 46.74 2.69
3836 4127 2.370189 ACCTTCAGAGGACAGGTTGAAG 59.630 50.000 0.00 6.19 46.74 3.02
3837 4128 2.370189 CCTTCAGAGGACAGGTTGAAGT 59.630 50.000 10.94 0.00 46.74 3.01
3838 4129 3.181450 CCTTCAGAGGACAGGTTGAAGTT 60.181 47.826 10.94 0.00 46.74 2.66
3839 4130 4.040461 CCTTCAGAGGACAGGTTGAAGTTA 59.960 45.833 10.94 0.00 46.74 2.24
3840 4131 4.873746 TCAGAGGACAGGTTGAAGTTAG 57.126 45.455 0.00 0.00 0.00 2.34
3841 4132 3.578716 TCAGAGGACAGGTTGAAGTTAGG 59.421 47.826 0.00 0.00 0.00 2.69
3842 4133 3.578716 CAGAGGACAGGTTGAAGTTAGGA 59.421 47.826 0.00 0.00 0.00 2.94
3843 4134 4.040461 CAGAGGACAGGTTGAAGTTAGGAA 59.960 45.833 0.00 0.00 0.00 3.36
3844 4135 4.284746 AGAGGACAGGTTGAAGTTAGGAAG 59.715 45.833 0.00 0.00 0.00 3.46
3845 4136 3.075148 GGACAGGTTGAAGTTAGGAAGC 58.925 50.000 0.00 0.00 0.00 3.86
3846 4137 3.244596 GGACAGGTTGAAGTTAGGAAGCT 60.245 47.826 0.00 0.00 0.00 3.74
3847 4138 4.020485 GGACAGGTTGAAGTTAGGAAGCTA 60.020 45.833 0.00 0.00 0.00 3.32
3848 4139 5.338463 GGACAGGTTGAAGTTAGGAAGCTAT 60.338 44.000 0.00 0.00 0.00 2.97
3849 4140 6.127140 GGACAGGTTGAAGTTAGGAAGCTATA 60.127 42.308 0.00 0.00 0.00 1.31
3850 4141 6.879400 ACAGGTTGAAGTTAGGAAGCTATAG 58.121 40.000 0.00 0.00 0.00 1.31
3851 4142 6.668283 ACAGGTTGAAGTTAGGAAGCTATAGA 59.332 38.462 3.21 0.00 0.00 1.98
3852 4143 7.147811 ACAGGTTGAAGTTAGGAAGCTATAGAG 60.148 40.741 3.21 0.00 0.00 2.43
3853 4144 7.068839 CAGGTTGAAGTTAGGAAGCTATAGAGA 59.931 40.741 3.21 0.00 0.00 3.10
3854 4145 7.787424 AGGTTGAAGTTAGGAAGCTATAGAGAT 59.213 37.037 3.21 0.00 0.00 2.75
3855 4146 8.085909 GGTTGAAGTTAGGAAGCTATAGAGATC 58.914 40.741 3.21 0.00 0.00 2.75
3856 4147 8.634444 GTTGAAGTTAGGAAGCTATAGAGATCA 58.366 37.037 3.21 0.00 0.00 2.92
3857 4148 8.768501 TGAAGTTAGGAAGCTATAGAGATCAA 57.231 34.615 3.21 0.00 0.00 2.57
3858 4149 9.201989 TGAAGTTAGGAAGCTATAGAGATCAAA 57.798 33.333 3.21 0.00 0.00 2.69
3859 4150 9.471084 GAAGTTAGGAAGCTATAGAGATCAAAC 57.529 37.037 3.21 6.58 0.00 2.93
3860 4151 7.958088 AGTTAGGAAGCTATAGAGATCAAACC 58.042 38.462 3.21 0.00 0.00 3.27
3861 4152 5.816955 AGGAAGCTATAGAGATCAAACCC 57.183 43.478 3.21 0.00 0.00 4.11
3862 4153 5.472347 AGGAAGCTATAGAGATCAAACCCT 58.528 41.667 3.21 0.00 0.00 4.34
3863 4154 5.908247 AGGAAGCTATAGAGATCAAACCCTT 59.092 40.000 3.21 0.00 0.00 3.95
3864 4155 5.994668 GGAAGCTATAGAGATCAAACCCTTG 59.005 44.000 3.21 0.00 0.00 3.61
3865 4156 4.967036 AGCTATAGAGATCAAACCCTTGC 58.033 43.478 3.21 0.00 32.14 4.01
3866 4157 3.743396 GCTATAGAGATCAAACCCTTGCG 59.257 47.826 3.21 0.00 32.14 4.85
3867 4158 4.501571 GCTATAGAGATCAAACCCTTGCGA 60.502 45.833 3.21 0.00 32.14 5.10
3868 4159 2.100605 AGAGATCAAACCCTTGCGAC 57.899 50.000 0.00 0.00 32.14 5.19
3869 4160 1.347707 AGAGATCAAACCCTTGCGACA 59.652 47.619 0.00 0.00 32.14 4.35
3870 4161 1.734465 GAGATCAAACCCTTGCGACAG 59.266 52.381 0.00 0.00 32.14 3.51
3891 4182 5.047306 ACAGAGCATGTTGTAGCTACTGTTA 60.047 40.000 23.84 8.93 41.72 2.41
3906 4197 2.100749 ACTGTTAAAGTTTGCTGTGGCC 59.899 45.455 0.00 0.00 34.57 5.36
3939 4230 2.854253 TGAGGTTGAAGCTCAGGGT 58.146 52.632 21.77 0.00 46.53 4.34
3940 4231 0.687354 TGAGGTTGAAGCTCAGGGTC 59.313 55.000 21.77 0.00 46.53 4.46
3941 4232 0.390472 GAGGTTGAAGCTCAGGGTCG 60.390 60.000 18.55 0.00 42.03 4.79
3942 4233 1.122019 AGGTTGAAGCTCAGGGTCGT 61.122 55.000 0.00 0.00 0.00 4.34
3943 4234 0.250338 GGTTGAAGCTCAGGGTCGTT 60.250 55.000 0.00 0.00 0.00 3.85
3966 4257 1.132689 ACAGGACCTTCAAGGAGAGGT 60.133 52.381 11.59 0.00 37.67 3.85
3986 4277 3.181465 GGTTGAGGATGGCGAAGAAGATA 60.181 47.826 0.00 0.00 0.00 1.98
3987 4278 4.442706 GTTGAGGATGGCGAAGAAGATAA 58.557 43.478 0.00 0.00 0.00 1.75
4027 4318 5.532779 GGTGGAGAGAAATTTGACTGAAACT 59.467 40.000 0.00 0.00 0.00 2.66
4028 4319 6.710744 GGTGGAGAGAAATTTGACTGAAACTA 59.289 38.462 0.00 0.00 0.00 2.24
4072 4363 8.058847 TCTGTAATAGTCTGCCCCATAAATTTT 58.941 33.333 0.00 0.00 0.00 1.82
4085 4376 5.746721 CCCATAAATTTTTGTAGTTAGCCGC 59.253 40.000 7.69 0.00 0.00 6.53
4128 4451 3.857157 TTGCTGTTTACAAGTCCTCCT 57.143 42.857 0.00 0.00 0.00 3.69
4148 4471 2.731451 CTGCGATCTTCGTTTGTTCTGA 59.269 45.455 0.00 0.00 42.81 3.27
4155 4478 7.072030 CGATCTTCGTTTGTTCTGATCTTTTT 58.928 34.615 0.00 0.00 34.72 1.94
4156 4479 8.221100 CGATCTTCGTTTGTTCTGATCTTTTTA 58.779 33.333 0.00 0.00 34.72 1.52
4157 4480 9.878599 GATCTTCGTTTGTTCTGATCTTTTTAA 57.121 29.630 0.00 0.00 0.00 1.52
4175 4498 3.704231 ATGTCGGGCAGGTGCATCC 62.704 63.158 4.01 0.00 44.36 3.51
4234 4557 6.217294 GGAGTTATGGAGTACTTGACATAGC 58.783 44.000 15.62 15.62 0.00 2.97
4236 4559 7.045126 AGTTATGGAGTACTTGACATAGCTC 57.955 40.000 18.17 12.13 33.86 4.09
4261 4584 2.938451 GCCTTCAATGCCCTTTAAATGC 59.062 45.455 3.55 3.55 0.00 3.56
4266 4589 4.577875 TCAATGCCCTTTAAATGCTTTGG 58.422 39.130 23.44 9.16 39.34 3.28
4274 4610 6.429692 GCCCTTTAAATGCTTTGGTAATGTTT 59.570 34.615 3.33 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 171 2.734723 GCGCGAACACAGCTCAGA 60.735 61.111 12.10 0.00 0.00 3.27
289 300 0.892755 TGGCGAAATACTCTCGTGGT 59.107 50.000 0.00 0.00 38.57 4.16
303 314 2.031560 CGGATCAATTCGATTTTGGCGA 59.968 45.455 8.30 0.00 33.17 5.54
743 769 9.665719 TTCTTAAAATTTGGTTCTCTTTTTGCT 57.334 25.926 0.00 0.00 0.00 3.91
776 803 9.313118 GTTCTTCTCTGAGAGAATTCCTTATTC 57.687 37.037 23.77 5.53 45.84 1.75
794 821 0.606604 TGTGCTACCCGGTTCTTCTC 59.393 55.000 0.00 0.00 0.00 2.87
795 822 0.320697 GTGTGCTACCCGGTTCTTCT 59.679 55.000 0.00 0.00 0.00 2.85
796 823 0.672711 GGTGTGCTACCCGGTTCTTC 60.673 60.000 0.00 0.00 44.15 2.87
797 824 1.373812 GGTGTGCTACCCGGTTCTT 59.626 57.895 0.00 0.00 44.15 2.52
798 825 3.066198 GGTGTGCTACCCGGTTCT 58.934 61.111 0.00 0.00 44.15 3.01
807 834 1.213537 GAACGTAGCGGGTGTGCTA 59.786 57.895 0.00 0.00 45.14 3.49
809 836 2.048503 AGAACGTAGCGGGTGTGC 60.049 61.111 0.00 0.00 0.00 4.57
810 837 1.800315 CGAGAACGTAGCGGGTGTG 60.800 63.158 0.00 0.00 34.56 3.82
811 838 1.518056 TTCGAGAACGTAGCGGGTGT 61.518 55.000 0.00 0.00 40.69 4.16
812 839 1.069378 GTTCGAGAACGTAGCGGGTG 61.069 60.000 0.00 0.00 40.69 4.61
813 840 1.211190 GTTCGAGAACGTAGCGGGT 59.789 57.895 0.00 0.00 40.69 5.28
814 841 0.387622 TTGTTCGAGAACGTAGCGGG 60.388 55.000 10.86 0.00 43.94 6.13
815 842 0.982673 CTTGTTCGAGAACGTAGCGG 59.017 55.000 10.86 0.00 43.94 5.52
816 843 0.362512 GCTTGTTCGAGAACGTAGCG 59.637 55.000 19.50 0.00 43.94 4.26
820 847 1.003866 GCTTTGCTTGTTCGAGAACGT 60.004 47.619 10.86 0.00 43.94 3.99
879 907 4.174762 CTCGTTTAGTCAGCTAGGGTTTC 58.825 47.826 0.00 0.00 0.00 2.78
929 957 1.152715 GTAGAGGAGGGGGACGAGG 60.153 68.421 0.00 0.00 0.00 4.63
930 958 1.152715 GGTAGAGGAGGGGGACGAG 60.153 68.421 0.00 0.00 0.00 4.18
931 959 3.013631 GGTAGAGGAGGGGGACGA 58.986 66.667 0.00 0.00 0.00 4.20
932 960 2.518825 CGGTAGAGGAGGGGGACG 60.519 72.222 0.00 0.00 0.00 4.79
933 961 2.838693 GCGGTAGAGGAGGGGGAC 60.839 72.222 0.00 0.00 0.00 4.46
934 962 4.153330 GGCGGTAGAGGAGGGGGA 62.153 72.222 0.00 0.00 0.00 4.81
1101 1139 0.390866 AGCTGTCGCAGATGGTGAAG 60.391 55.000 10.46 0.00 40.67 3.02
1245 1283 2.951785 TACGGGGTGGGGGAGGTA 60.952 66.667 0.00 0.00 0.00 3.08
1272 1310 0.678048 AGCTTTTAGCCCAGCTTCGG 60.678 55.000 0.00 0.00 44.28 4.30
1289 1327 0.654683 AAAATCGCATCGCTGAGAGC 59.345 50.000 0.00 0.00 34.53 4.09
1362 1400 2.159707 CCAATAAACGTCAGAACCGCAG 60.160 50.000 0.00 0.00 0.00 5.18
1618 1664 4.168101 AGTTCCATCTACTCAAGACCCAA 58.832 43.478 0.00 0.00 36.93 4.12
1619 1665 3.791320 AGTTCCATCTACTCAAGACCCA 58.209 45.455 0.00 0.00 36.93 4.51
1620 1666 4.020128 ACAAGTTCCATCTACTCAAGACCC 60.020 45.833 0.00 0.00 36.93 4.46
1724 1773 1.002033 CTAAGCGCTTCCATCCATTGC 60.002 52.381 28.82 0.00 0.00 3.56
1825 1917 6.486657 ACAAATACATGGGCTGTCATATGTAC 59.513 38.462 9.70 0.80 38.42 2.90
1836 1930 2.632028 TGCAAACACAAATACATGGGCT 59.368 40.909 0.00 0.00 0.00 5.19
1892 1986 5.596845 ACAACACCACCAAACATAACATTC 58.403 37.500 0.00 0.00 0.00 2.67
1944 2038 1.905637 TGGTTAGAGCGACTCTGTCA 58.094 50.000 16.48 10.27 41.37 3.58
1954 2048 5.470437 GCTACCCTTAATCATTGGTTAGAGC 59.530 44.000 0.00 0.00 32.27 4.09
1965 2059 4.917385 TCTTTTGCTGCTACCCTTAATCA 58.083 39.130 0.00 0.00 0.00 2.57
1987 2081 1.478510 CTAGTGACCTCGCTGGATGTT 59.521 52.381 0.00 0.00 37.16 2.71
2077 2171 3.136123 CCATGCGAGCAAGGTGGG 61.136 66.667 10.83 0.90 30.89 4.61
2302 2396 5.832539 TCTTCAAGTCCAGAGGAATTTCT 57.167 39.130 0.00 0.00 37.96 2.52
2338 2432 6.056428 ACGTGAAACTTACATCCAACTTTC 57.944 37.500 0.00 0.00 31.75 2.62
2390 2607 7.561722 AGCTACCAGATCAACAGAGTAGATTTA 59.438 37.037 0.00 0.00 31.00 1.40
2396 2613 6.188407 AGTAAGCTACCAGATCAACAGAGTA 58.812 40.000 0.00 0.00 0.00 2.59
2479 2696 8.892723 CAATACCTCATTTAGTTCAGTGCAATA 58.107 33.333 0.00 0.00 0.00 1.90
2486 2703 8.492673 TGCTTACAATACCTCATTTAGTTCAG 57.507 34.615 0.00 0.00 0.00 3.02
2505 2722 6.528072 GGTTTTTGTTGCTCATAGATGCTTAC 59.472 38.462 0.00 0.00 0.00 2.34
2538 2756 6.554334 TTTACTGGCAGACAAGTTATTGAC 57.446 37.500 23.66 0.00 38.83 3.18
2576 2797 2.855209 ACAGAAGAGTTCAGCAGCAT 57.145 45.000 0.00 0.00 0.00 3.79
2577 2798 2.627515 AACAGAAGAGTTCAGCAGCA 57.372 45.000 0.00 0.00 0.00 4.41
2578 2799 3.978718 AAAACAGAAGAGTTCAGCAGC 57.021 42.857 0.00 0.00 0.00 5.25
2579 2800 5.032863 CACAAAAACAGAAGAGTTCAGCAG 58.967 41.667 0.00 0.00 0.00 4.24
2580 2801 4.458989 ACACAAAAACAGAAGAGTTCAGCA 59.541 37.500 0.00 0.00 0.00 4.41
2581 2802 4.986622 ACACAAAAACAGAAGAGTTCAGC 58.013 39.130 0.00 0.00 0.00 4.26
2582 2803 8.964420 TTTTACACAAAAACAGAAGAGTTCAG 57.036 30.769 0.00 0.00 32.05 3.02
2583 2804 9.921637 ATTTTTACACAAAAACAGAAGAGTTCA 57.078 25.926 0.00 0.00 44.26 3.18
2615 2836 3.826157 CCTTCCACTAAAATTGCCAGTCA 59.174 43.478 0.00 0.00 0.00 3.41
2787 3008 1.750206 TCAACAGCAACAGCAACATGT 59.250 42.857 0.00 0.00 33.96 3.21
2788 3009 2.121786 GTCAACAGCAACAGCAACATG 58.878 47.619 0.00 0.00 0.00 3.21
2958 3184 6.241385 GTCAAGATACAAAGTACATGAACGC 58.759 40.000 0.00 0.00 0.00 4.84
3196 3425 5.880332 GTCCTGCAACAGTAAGGAAATATGA 59.120 40.000 1.91 0.00 41.70 2.15
3271 3500 1.004440 GGTGTTCAGCTTCTCGGCT 60.004 57.895 0.00 0.00 44.10 5.52
3351 3582 3.354089 AACGAAAACCAAGCACAGATG 57.646 42.857 0.00 0.00 0.00 2.90
3352 3583 3.705604 CAAACGAAAACCAAGCACAGAT 58.294 40.909 0.00 0.00 0.00 2.90
3476 3728 6.139679 ACTAAATCCAATGGAAAGGTCTGA 57.860 37.500 5.89 0.00 34.34 3.27
3502 3760 7.759489 AATATTCAGCCAGAAACAAAGTACA 57.241 32.000 0.00 0.00 40.22 2.90
3534 3792 6.239008 CCAAGAAAAACAAAGCCAGTATCAGA 60.239 38.462 0.00 0.00 0.00 3.27
3554 3835 4.895889 TCTCTGACTGAAAGAGAACCAAGA 59.104 41.667 10.27 0.00 45.56 3.02
3555 3836 5.207110 TCTCTGACTGAAAGAGAACCAAG 57.793 43.478 10.27 0.00 45.56 3.61
3654 3937 2.096248 ACACGCTTTTGTTTCAAGGGA 58.904 42.857 3.97 0.00 37.57 4.20
3680 3963 3.629398 CACCATTTGGCATAGACTCTTCC 59.371 47.826 0.00 0.00 39.32 3.46
3701 3992 3.772853 AAGTGCCTCTGCGTTGCCA 62.773 57.895 0.00 0.00 41.78 4.92
3750 4041 3.057548 CACCGCAATGCTCTGCCA 61.058 61.111 2.94 0.00 39.26 4.92
3761 4052 2.889606 ATGTACACCAGCCACCGCA 61.890 57.895 0.00 0.00 37.52 5.69
3762 4053 2.046314 ATGTACACCAGCCACCGC 60.046 61.111 0.00 0.00 0.00 5.68
3763 4054 0.321210 TTCATGTACACCAGCCACCG 60.321 55.000 0.00 0.00 0.00 4.94
3764 4055 1.003118 TCTTCATGTACACCAGCCACC 59.997 52.381 0.00 0.00 0.00 4.61
3765 4056 2.472695 TCTTCATGTACACCAGCCAC 57.527 50.000 0.00 0.00 0.00 5.01
3766 4057 2.571202 TCATCTTCATGTACACCAGCCA 59.429 45.455 0.00 0.00 0.00 4.75
3767 4058 3.201290 CTCATCTTCATGTACACCAGCC 58.799 50.000 0.00 0.00 0.00 4.85
3768 4059 3.201290 CCTCATCTTCATGTACACCAGC 58.799 50.000 0.00 0.00 0.00 4.85
3769 4060 4.478206 ACCTCATCTTCATGTACACCAG 57.522 45.455 0.00 0.00 0.00 4.00
3770 4061 4.285775 TCAACCTCATCTTCATGTACACCA 59.714 41.667 0.00 0.00 0.00 4.17
3771 4062 4.832248 TCAACCTCATCTTCATGTACACC 58.168 43.478 0.00 0.00 0.00 4.16
3772 4063 5.163814 GCTTCAACCTCATCTTCATGTACAC 60.164 44.000 0.00 0.00 0.00 2.90
3773 4064 4.937620 GCTTCAACCTCATCTTCATGTACA 59.062 41.667 0.00 0.00 0.00 2.90
3774 4065 5.181748 AGCTTCAACCTCATCTTCATGTAC 58.818 41.667 0.00 0.00 0.00 2.90
3775 4066 5.426689 AGCTTCAACCTCATCTTCATGTA 57.573 39.130 0.00 0.00 0.00 2.29
3776 4067 4.298103 AGCTTCAACCTCATCTTCATGT 57.702 40.909 0.00 0.00 0.00 3.21
3777 4068 5.296283 CCTAAGCTTCAACCTCATCTTCATG 59.704 44.000 0.00 0.00 0.00 3.07
3778 4069 5.435291 CCTAAGCTTCAACCTCATCTTCAT 58.565 41.667 0.00 0.00 0.00 2.57
3779 4070 4.323792 CCCTAAGCTTCAACCTCATCTTCA 60.324 45.833 0.00 0.00 0.00 3.02
3780 4071 4.195416 CCCTAAGCTTCAACCTCATCTTC 58.805 47.826 0.00 0.00 0.00 2.87
3781 4072 3.054065 CCCCTAAGCTTCAACCTCATCTT 60.054 47.826 0.00 0.00 0.00 2.40
3782 4073 2.507471 CCCCTAAGCTTCAACCTCATCT 59.493 50.000 0.00 0.00 0.00 2.90
3783 4074 2.924421 CCCCTAAGCTTCAACCTCATC 58.076 52.381 0.00 0.00 0.00 2.92
3784 4075 1.064389 GCCCCTAAGCTTCAACCTCAT 60.064 52.381 0.00 0.00 0.00 2.90
3785 4076 0.328258 GCCCCTAAGCTTCAACCTCA 59.672 55.000 0.00 0.00 0.00 3.86
3786 4077 0.744771 CGCCCCTAAGCTTCAACCTC 60.745 60.000 0.00 0.00 0.00 3.85
3787 4078 1.299976 CGCCCCTAAGCTTCAACCT 59.700 57.895 0.00 0.00 0.00 3.50
3788 4079 1.002502 ACGCCCCTAAGCTTCAACC 60.003 57.895 0.00 0.00 0.00 3.77
3789 4080 1.359459 CGACGCCCCTAAGCTTCAAC 61.359 60.000 0.00 0.00 30.81 3.18
3790 4081 1.079405 CGACGCCCCTAAGCTTCAA 60.079 57.895 0.00 0.00 30.81 2.69
3791 4082 2.577059 CGACGCCCCTAAGCTTCA 59.423 61.111 0.00 0.00 30.81 3.02
3792 4083 2.029307 ATCCGACGCCCCTAAGCTTC 62.029 60.000 0.00 0.00 0.00 3.86
3793 4084 0.757935 TATCCGACGCCCCTAAGCTT 60.758 55.000 3.48 3.48 0.00 3.74
3794 4085 1.152610 TATCCGACGCCCCTAAGCT 60.153 57.895 0.00 0.00 0.00 3.74
3795 4086 1.289380 CTATCCGACGCCCCTAAGC 59.711 63.158 0.00 0.00 0.00 3.09
3796 4087 0.538977 TCCTATCCGACGCCCCTAAG 60.539 60.000 0.00 0.00 0.00 2.18
3797 4088 0.825010 GTCCTATCCGACGCCCCTAA 60.825 60.000 0.00 0.00 0.00 2.69
3798 4089 1.228367 GTCCTATCCGACGCCCCTA 60.228 63.158 0.00 0.00 0.00 3.53
3799 4090 2.521224 GTCCTATCCGACGCCCCT 60.521 66.667 0.00 0.00 0.00 4.79
3800 4091 3.613689 GGTCCTATCCGACGCCCC 61.614 72.222 0.00 0.00 33.30 5.80
3801 4092 2.085042 GAAGGTCCTATCCGACGCCC 62.085 65.000 0.00 0.00 33.30 6.13
3802 4093 1.363080 GAAGGTCCTATCCGACGCC 59.637 63.158 0.00 0.00 33.30 5.68
3803 4094 0.030908 CTGAAGGTCCTATCCGACGC 59.969 60.000 0.00 0.00 33.30 5.19
3804 4095 1.604755 CTCTGAAGGTCCTATCCGACG 59.395 57.143 0.00 0.00 33.30 5.12
3805 4096 1.957877 CCTCTGAAGGTCCTATCCGAC 59.042 57.143 0.00 0.00 37.94 4.79
3806 4097 1.850998 TCCTCTGAAGGTCCTATCCGA 59.149 52.381 0.00 0.00 43.82 4.55
3807 4098 1.957877 GTCCTCTGAAGGTCCTATCCG 59.042 57.143 0.00 0.00 43.82 4.18
3808 4099 2.962421 CTGTCCTCTGAAGGTCCTATCC 59.038 54.545 0.00 0.00 43.82 2.59
3809 4100 2.962421 CCTGTCCTCTGAAGGTCCTATC 59.038 54.545 0.00 0.00 43.82 2.08
3810 4101 2.316372 ACCTGTCCTCTGAAGGTCCTAT 59.684 50.000 0.00 0.00 40.34 2.57
3811 4102 1.717077 ACCTGTCCTCTGAAGGTCCTA 59.283 52.381 0.00 0.00 40.34 2.94
3812 4103 0.489567 ACCTGTCCTCTGAAGGTCCT 59.510 55.000 0.00 0.00 40.34 3.85
3813 4104 1.002544 CAACCTGTCCTCTGAAGGTCC 59.997 57.143 0.00 0.00 43.62 4.46
3814 4105 1.971357 TCAACCTGTCCTCTGAAGGTC 59.029 52.381 0.00 0.00 43.62 3.85
3815 4106 2.103153 TCAACCTGTCCTCTGAAGGT 57.897 50.000 0.00 0.00 46.40 3.50
3816 4107 2.370189 ACTTCAACCTGTCCTCTGAAGG 59.630 50.000 13.52 0.00 45.88 3.46
3817 4108 3.760580 ACTTCAACCTGTCCTCTGAAG 57.239 47.619 8.69 8.69 46.62 3.02
3818 4109 4.040461 CCTAACTTCAACCTGTCCTCTGAA 59.960 45.833 0.00 0.00 0.00 3.02
3819 4110 3.578716 CCTAACTTCAACCTGTCCTCTGA 59.421 47.826 0.00 0.00 0.00 3.27
3820 4111 3.578716 TCCTAACTTCAACCTGTCCTCTG 59.421 47.826 0.00 0.00 0.00 3.35
3821 4112 3.858135 TCCTAACTTCAACCTGTCCTCT 58.142 45.455 0.00 0.00 0.00 3.69
3822 4113 4.570930 CTTCCTAACTTCAACCTGTCCTC 58.429 47.826 0.00 0.00 0.00 3.71
3823 4114 3.244596 GCTTCCTAACTTCAACCTGTCCT 60.245 47.826 0.00 0.00 0.00 3.85
3824 4115 3.075148 GCTTCCTAACTTCAACCTGTCC 58.925 50.000 0.00 0.00 0.00 4.02
3825 4116 4.009370 AGCTTCCTAACTTCAACCTGTC 57.991 45.455 0.00 0.00 0.00 3.51
3826 4117 5.763876 ATAGCTTCCTAACTTCAACCTGT 57.236 39.130 0.00 0.00 0.00 4.00
3827 4118 7.068839 TCTCTATAGCTTCCTAACTTCAACCTG 59.931 40.741 0.00 0.00 0.00 4.00
3828 4119 7.126733 TCTCTATAGCTTCCTAACTTCAACCT 58.873 38.462 0.00 0.00 0.00 3.50
3829 4120 7.349412 TCTCTATAGCTTCCTAACTTCAACC 57.651 40.000 0.00 0.00 0.00 3.77
3830 4121 8.634444 TGATCTCTATAGCTTCCTAACTTCAAC 58.366 37.037 0.00 0.00 0.00 3.18
3831 4122 8.768501 TGATCTCTATAGCTTCCTAACTTCAA 57.231 34.615 0.00 0.00 0.00 2.69
3832 4123 8.768501 TTGATCTCTATAGCTTCCTAACTTCA 57.231 34.615 0.00 0.00 0.00 3.02
3833 4124 9.471084 GTTTGATCTCTATAGCTTCCTAACTTC 57.529 37.037 0.00 0.00 0.00 3.01
3834 4125 8.425703 GGTTTGATCTCTATAGCTTCCTAACTT 58.574 37.037 0.00 0.00 0.00 2.66
3835 4126 7.015779 GGGTTTGATCTCTATAGCTTCCTAACT 59.984 40.741 0.00 0.00 0.00 2.24
3836 4127 7.015779 AGGGTTTGATCTCTATAGCTTCCTAAC 59.984 40.741 0.00 0.00 0.00 2.34
3837 4128 7.076446 AGGGTTTGATCTCTATAGCTTCCTAA 58.924 38.462 0.00 0.00 0.00 2.69
3838 4129 6.625267 AGGGTTTGATCTCTATAGCTTCCTA 58.375 40.000 0.00 0.00 0.00 2.94
3839 4130 5.472347 AGGGTTTGATCTCTATAGCTTCCT 58.528 41.667 0.00 0.00 0.00 3.36
3840 4131 5.816955 AGGGTTTGATCTCTATAGCTTCC 57.183 43.478 0.00 0.00 0.00 3.46
3841 4132 5.468409 GCAAGGGTTTGATCTCTATAGCTTC 59.532 44.000 0.00 0.00 36.36 3.86
3842 4133 5.372373 GCAAGGGTTTGATCTCTATAGCTT 58.628 41.667 0.00 0.00 36.36 3.74
3843 4134 4.502259 CGCAAGGGTTTGATCTCTATAGCT 60.502 45.833 0.00 0.00 36.36 3.32
3844 4135 3.743396 CGCAAGGGTTTGATCTCTATAGC 59.257 47.826 0.00 0.00 36.36 2.97
3845 4136 4.985409 GTCGCAAGGGTTTGATCTCTATAG 59.015 45.833 0.00 0.00 36.36 1.31
3846 4137 4.404394 TGTCGCAAGGGTTTGATCTCTATA 59.596 41.667 0.00 0.00 36.36 1.31
3847 4138 3.197766 TGTCGCAAGGGTTTGATCTCTAT 59.802 43.478 0.00 0.00 36.36 1.98
3848 4139 2.565391 TGTCGCAAGGGTTTGATCTCTA 59.435 45.455 0.00 0.00 36.36 2.43
3849 4140 1.347707 TGTCGCAAGGGTTTGATCTCT 59.652 47.619 0.00 0.00 36.36 3.10
3850 4141 1.734465 CTGTCGCAAGGGTTTGATCTC 59.266 52.381 0.00 0.00 36.36 2.75
3851 4142 1.347707 TCTGTCGCAAGGGTTTGATCT 59.652 47.619 0.00 0.00 36.36 2.75
3852 4143 1.734465 CTCTGTCGCAAGGGTTTGATC 59.266 52.381 0.00 0.00 36.36 2.92
3853 4144 1.813513 CTCTGTCGCAAGGGTTTGAT 58.186 50.000 0.00 0.00 36.36 2.57
3854 4145 0.884704 GCTCTGTCGCAAGGGTTTGA 60.885 55.000 0.00 0.00 36.36 2.69
3855 4146 1.165907 TGCTCTGTCGCAAGGGTTTG 61.166 55.000 0.00 0.00 36.89 2.93
3856 4147 0.250901 ATGCTCTGTCGCAAGGGTTT 60.251 50.000 0.00 0.00 44.06 3.27
3857 4148 0.957395 CATGCTCTGTCGCAAGGGTT 60.957 55.000 0.00 0.00 44.06 4.11
3858 4149 1.376424 CATGCTCTGTCGCAAGGGT 60.376 57.895 0.00 0.00 44.06 4.34
3859 4150 0.957395 AACATGCTCTGTCGCAAGGG 60.957 55.000 0.00 0.00 44.06 3.95
3860 4151 0.167470 CAACATGCTCTGTCGCAAGG 59.833 55.000 0.00 0.00 44.06 3.61
3861 4152 0.870393 ACAACATGCTCTGTCGCAAG 59.130 50.000 0.00 0.00 44.06 4.01
3862 4153 2.068519 CTACAACATGCTCTGTCGCAA 58.931 47.619 0.00 0.00 44.06 4.85
3863 4154 1.713597 CTACAACATGCTCTGTCGCA 58.286 50.000 0.00 0.00 45.10 5.10
3864 4155 0.371645 GCTACAACATGCTCTGTCGC 59.628 55.000 0.00 0.00 36.98 5.19
3865 4156 2.001812 AGCTACAACATGCTCTGTCG 57.998 50.000 0.00 0.00 36.98 4.35
3866 4157 3.862267 CAGTAGCTACAACATGCTCTGTC 59.138 47.826 25.28 0.00 40.35 3.51
3867 4158 3.259374 ACAGTAGCTACAACATGCTCTGT 59.741 43.478 25.28 14.05 39.89 3.41
3868 4159 3.854666 ACAGTAGCTACAACATGCTCTG 58.145 45.455 25.28 13.44 40.35 3.35
3869 4160 4.543590 AACAGTAGCTACAACATGCTCT 57.456 40.909 25.28 0.00 40.35 4.09
3870 4161 6.369065 ACTTTAACAGTAGCTACAACATGCTC 59.631 38.462 25.28 0.00 40.35 4.26
3891 4182 3.128375 CCGGCCACAGCAAACTTT 58.872 55.556 2.24 0.00 42.56 2.66
3906 4197 1.202417 ACCTCATCTTCATGTACGCCG 60.202 52.381 0.00 0.00 0.00 6.46
3939 4230 1.070134 CTTGAAGGTCCTGTCCAACGA 59.930 52.381 0.00 0.00 0.00 3.85
3940 4231 1.512926 CTTGAAGGTCCTGTCCAACG 58.487 55.000 0.00 0.00 0.00 4.10
3941 4232 1.420138 TCCTTGAAGGTCCTGTCCAAC 59.580 52.381 11.60 0.00 36.53 3.77
3942 4233 1.699634 CTCCTTGAAGGTCCTGTCCAA 59.300 52.381 11.60 0.00 36.53 3.53
3943 4234 1.132849 TCTCCTTGAAGGTCCTGTCCA 60.133 52.381 11.60 0.00 36.53 4.02
3966 4257 4.753516 TTATCTTCTTCGCCATCCTCAA 57.246 40.909 0.00 0.00 0.00 3.02
3986 4277 1.134280 CACCGCTGGATCATCCTCTTT 60.134 52.381 4.96 0.00 37.46 2.52
3987 4278 0.467384 CACCGCTGGATCATCCTCTT 59.533 55.000 4.96 0.00 37.46 2.85
4036 4327 3.322254 AGACTATTACAGATTCGCCTGGG 59.678 47.826 0.00 0.00 38.44 4.45
4037 4328 4.302455 CAGACTATTACAGATTCGCCTGG 58.698 47.826 0.00 0.00 38.44 4.45
4072 4363 0.317799 TTGACCGCGGCTAACTACAA 59.682 50.000 28.58 16.34 0.00 2.41
4085 4376 1.557443 AAGCGCTCGAAACTTGACCG 61.557 55.000 12.06 0.00 0.00 4.79
4101 4392 3.383761 ACTTGTAAACAGCAATGCAAGC 58.616 40.909 8.35 6.40 41.25 4.01
4128 4451 2.749776 TCAGAACAAACGAAGATCGCA 58.250 42.857 0.00 0.00 45.12 5.10
4148 4471 3.443681 CACCTGCCCGACATTAAAAAGAT 59.556 43.478 0.00 0.00 0.00 2.40
4155 4478 0.463654 GATGCACCTGCCCGACATTA 60.464 55.000 0.00 0.00 41.18 1.90
4156 4479 1.750399 GATGCACCTGCCCGACATT 60.750 57.895 0.00 0.00 41.18 2.71
4157 4480 2.124570 GATGCACCTGCCCGACAT 60.125 61.111 0.00 0.00 41.18 3.06
4209 4532 5.615925 ATGTCAAGTACTCCATAACTCCC 57.384 43.478 0.00 0.00 0.00 4.30
4214 4537 5.304614 GGGAGCTATGTCAAGTACTCCATAA 59.695 44.000 8.94 0.00 44.47 1.90
4216 4539 3.643792 GGGAGCTATGTCAAGTACTCCAT 59.356 47.826 8.94 1.94 44.47 3.41
4217 4540 3.031736 GGGAGCTATGTCAAGTACTCCA 58.968 50.000 8.94 0.00 44.47 3.86
4218 4541 3.031736 TGGGAGCTATGTCAAGTACTCC 58.968 50.000 0.00 0.00 42.42 3.85
4219 4542 3.491792 GCTGGGAGCTATGTCAAGTACTC 60.492 52.174 0.00 0.00 38.45 2.59
4220 4543 2.432510 GCTGGGAGCTATGTCAAGTACT 59.567 50.000 0.00 0.00 38.45 2.73
4221 4544 2.483889 GGCTGGGAGCTATGTCAAGTAC 60.484 54.545 0.00 0.00 41.99 2.73
4234 4557 1.755783 GGGCATTGAAGGCTGGGAG 60.756 63.158 0.72 0.00 0.00 4.30
4236 4559 0.906282 AAAGGGCATTGAAGGCTGGG 60.906 55.000 0.72 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.