Multiple sequence alignment - TraesCS7A01G494500

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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 TraesCS7A01G494500 chr7A 100.000 2981 0 0 940 3920 683096614 683099594 0.000000e+00 5505.0
1 TraesCS7A01G494500 chr7A 100.000 523 0 0 1 523 683095675 683096197 0.000000e+00 966.0
2 TraesCS7A01G494500 chr7B 94.647 2914 107 14 940 3839 671258413 671255535 0.000000e+00 4471.0
3 TraesCS7A01G494500 chr7B 89.682 1037 58 14 2817 3839 671066247 671065246 0.000000e+00 1277.0
4 TraesCS7A01G494500 chr7B 89.479 1036 61 14 2817 3839 671001328 671000328 0.000000e+00 1266.0
5 TraesCS7A01G494500 chr7B 89.296 1037 62 14 2817 3839 671184072 671183071 0.000000e+00 1254.0
6 TraesCS7A01G494500 chr7B 85.227 352 29 15 174 523 671259419 671259089 1.350000e-89 340.0
7 TraesCS7A01G494500 chr7B 91.195 159 14 0 1 159 110916751 110916909 2.370000e-52 217.0
8 TraesCS7A01G494500 chr7B 95.238 84 4 0 3833 3916 670999536 670999453 2.460000e-27 134.0
9 TraesCS7A01G494500 chr7B 95.238 84 4 0 3833 3916 671064454 671064371 2.460000e-27 134.0
10 TraesCS7A01G494500 chr7D 96.782 2641 78 4 963 3597 591854453 591857092 0.000000e+00 4399.0
11 TraesCS7A01G494500 chr7D 87.087 333 26 8 191 523 591853715 591854030 1.040000e-95 361.0
12 TraesCS7A01G494500 chr7D 94.860 214 10 1 3627 3839 591857087 591857300 2.260000e-87 333.0
13 TraesCS7A01G494500 chr1D 92.955 2328 137 9 949 3259 463863510 463865827 0.000000e+00 3365.0
14 TraesCS7A01G494500 chr1D 81.287 171 14 9 3433 3587 463866326 463866494 5.320000e-24 122.0
15 TraesCS7A01G494500 chr1A 92.206 2117 140 10 1165 3259 555825060 555827173 0.000000e+00 2972.0
16 TraesCS7A01G494500 chr1B 94.662 1611 85 1 949 2559 639033862 639035471 0.000000e+00 2497.0
17 TraesCS7A01G494500 chr1B 88.076 738 60 11 2557 3272 639043609 639044340 0.000000e+00 850.0
18 TraesCS7A01G494500 chrUn 89.403 1038 60 15 2817 3839 147154942 147153940 0.000000e+00 1262.0
19 TraesCS7A01G494500 chrUn 89.296 1037 62 14 2817 3839 147236759 147235758 0.000000e+00 1254.0
20 TraesCS7A01G494500 chrUn 89.296 1037 62 14 2817 3839 147306237 147305236 0.000000e+00 1254.0
21 TraesCS7A01G494500 chrUn 95.238 84 4 0 3833 3916 147153164 147153081 2.460000e-27 134.0
22 TraesCS7A01G494500 chr5B 91.875 160 11 2 2 161 90518068 90518225 5.100000e-54 222.0
23 TraesCS7A01G494500 chr6A 90.476 168 11 4 1 166 594612672 594612508 2.370000e-52 217.0
24 TraesCS7A01G494500 chr5D 85.987 157 9 5 1 157 494688830 494688973 5.240000e-34 156.0
25 TraesCS7A01G494500 chr2D 94.595 37 2 0 119 155 5169644 5169680 1.520000e-04 58.4


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 TraesCS7A01G494500 chr7A 683095675 683099594 3919 False 3235.500000 5505 100.000000 1 3920 2 chr7A.!!$F1 3919
1 TraesCS7A01G494500 chr7B 671255535 671259419 3884 True 2405.500000 4471 89.937000 174 3839 2 chr7B.!!$R4 3665
2 TraesCS7A01G494500 chr7B 671183071 671184072 1001 True 1254.000000 1254 89.296000 2817 3839 1 chr7B.!!$R1 1022
3 TraesCS7A01G494500 chr7B 671064371 671066247 1876 True 705.500000 1277 92.460000 2817 3916 2 chr7B.!!$R3 1099
4 TraesCS7A01G494500 chr7B 670999453 671001328 1875 True 700.000000 1266 92.358500 2817 3916 2 chr7B.!!$R2 1099
5 TraesCS7A01G494500 chr7D 591853715 591857300 3585 False 1697.666667 4399 92.909667 191 3839 3 chr7D.!!$F1 3648
6 TraesCS7A01G494500 chr1D 463863510 463866494 2984 False 1743.500000 3365 87.121000 949 3587 2 chr1D.!!$F1 2638
7 TraesCS7A01G494500 chr1A 555825060 555827173 2113 False 2972.000000 2972 92.206000 1165 3259 1 chr1A.!!$F1 2094
8 TraesCS7A01G494500 chr1B 639033862 639035471 1609 False 2497.000000 2497 94.662000 949 2559 1 chr1B.!!$F1 1610
9 TraesCS7A01G494500 chr1B 639043609 639044340 731 False 850.000000 850 88.076000 2557 3272 1 chr1B.!!$F2 715
10 TraesCS7A01G494500 chrUn 147235758 147236759 1001 True 1254.000000 1254 89.296000 2817 3839 1 chrUn.!!$R1 1022
11 TraesCS7A01G494500 chrUn 147305236 147306237 1001 True 1254.000000 1254 89.296000 2817 3839 1 chrUn.!!$R2 1022
12 TraesCS7A01G494500 chrUn 147153081 147154942 1861 True 698.000000 1262 92.320500 2817 3916 2 chrUn.!!$R3 1099

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
36 37 0.035820 GGCCAACACTAATGACGGGA 60.036 55.0 0.00 0.0 0.00 5.14 F
317 319 0.115349 AGCCTGTCTGGTGGTCTAGT 59.885 55.0 0.00 0.0 38.35 2.57 F
1415 1683 0.110486 GGGAGGAGGTGCACAAGAAA 59.890 55.0 20.43 0.0 0.00 2.52 F
1612 1880 0.883814 AGCTCAGTTCACAGTGCAGC 60.884 55.0 0.00 0.0 31.60 5.25 F
1904 2172 1.484444 GGGCAGAGGAGACAGTGGTT 61.484 60.0 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1528 1.043816 ATCGCATCGGAGAGGAACAT 58.956 50.000 0.0 0.0 43.16 2.71 R
1556 1824 2.342406 TCACCTCCAAATCCCTCTCA 57.658 50.000 0.0 0.0 0.00 3.27 R
2876 3149 2.548480 AGCTTTGTGTTTCGAACTAGGC 59.452 45.455 0.0 0.0 0.00 3.93 R
2880 3153 3.006940 TGTGAGCTTTGTGTTTCGAACT 58.993 40.909 0.0 0.0 0.00 3.01 R
3747 4416 1.365028 AGGAACAGGGGGAACTAGCTA 59.635 52.381 0.0 0.0 0.00 3.32 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
19 20 0.451783 CATGGGTTAGCTGAAACGGC 59.548 55.000 0.00 0.00 35.73 5.68
20 21 0.679960 ATGGGTTAGCTGAAACGGCC 60.680 55.000 0.00 0.00 36.20 6.13
21 22 1.302993 GGGTTAGCTGAAACGGCCA 60.303 57.895 2.24 0.00 36.20 5.36
22 23 0.891904 GGGTTAGCTGAAACGGCCAA 60.892 55.000 2.24 0.00 36.20 4.52
23 24 0.240145 GGTTAGCTGAAACGGCCAAC 59.760 55.000 2.24 5.57 36.81 3.77
24 25 0.948678 GTTAGCTGAAACGGCCAACA 59.051 50.000 2.24 0.00 37.33 3.33
25 26 0.948678 TTAGCTGAAACGGCCAACAC 59.051 50.000 2.24 0.00 36.20 3.32
26 27 0.107831 TAGCTGAAACGGCCAACACT 59.892 50.000 2.24 0.00 36.20 3.55
27 28 0.107831 AGCTGAAACGGCCAACACTA 59.892 50.000 2.24 0.00 36.20 2.74
28 29 0.948678 GCTGAAACGGCCAACACTAA 59.051 50.000 2.24 0.00 0.00 2.24
29 30 1.539827 GCTGAAACGGCCAACACTAAT 59.460 47.619 2.24 0.00 0.00 1.73
30 31 2.668279 GCTGAAACGGCCAACACTAATG 60.668 50.000 2.24 0.00 0.00 1.90
31 32 2.811431 CTGAAACGGCCAACACTAATGA 59.189 45.455 2.24 0.00 0.00 2.57
32 33 2.550606 TGAAACGGCCAACACTAATGAC 59.449 45.455 2.24 0.00 0.00 3.06
33 34 1.153353 AACGGCCAACACTAATGACG 58.847 50.000 2.24 0.00 0.00 4.35
34 35 0.672401 ACGGCCAACACTAATGACGG 60.672 55.000 2.24 0.00 0.00 4.79
35 36 1.366111 CGGCCAACACTAATGACGGG 61.366 60.000 2.24 0.00 0.00 5.28
36 37 0.035820 GGCCAACACTAATGACGGGA 60.036 55.000 0.00 0.00 0.00 5.14
37 38 1.408266 GGCCAACACTAATGACGGGAT 60.408 52.381 0.00 0.00 0.00 3.85
38 39 2.365582 GCCAACACTAATGACGGGATT 58.634 47.619 0.00 0.00 0.00 3.01
39 40 3.537580 GCCAACACTAATGACGGGATTA 58.462 45.455 0.00 0.00 0.00 1.75
40 41 3.942748 GCCAACACTAATGACGGGATTAA 59.057 43.478 0.00 0.00 0.00 1.40
41 42 4.578928 GCCAACACTAATGACGGGATTAAT 59.421 41.667 0.00 0.00 0.00 1.40
42 43 5.067283 GCCAACACTAATGACGGGATTAATT 59.933 40.000 0.00 0.00 0.00 1.40
43 44 6.405397 GCCAACACTAATGACGGGATTAATTT 60.405 38.462 0.00 0.00 0.00 1.82
44 45 7.193595 CCAACACTAATGACGGGATTAATTTC 58.806 38.462 0.00 0.00 0.00 2.17
45 46 6.937436 ACACTAATGACGGGATTAATTTCC 57.063 37.500 0.00 0.00 34.83 3.13
46 47 6.419791 ACACTAATGACGGGATTAATTTCCA 58.580 36.000 8.78 0.00 37.53 3.53
47 48 6.887545 ACACTAATGACGGGATTAATTTCCAA 59.112 34.615 8.78 0.00 37.53 3.53
48 49 7.394923 ACACTAATGACGGGATTAATTTCCAAA 59.605 33.333 8.78 0.00 37.53 3.28
49 50 8.413229 CACTAATGACGGGATTAATTTCCAAAT 58.587 33.333 8.78 0.00 37.53 2.32
50 51 8.977412 ACTAATGACGGGATTAATTTCCAAATT 58.023 29.630 2.92 2.92 41.24 1.82
51 52 9.463443 CTAATGACGGGATTAATTTCCAAATTC 57.537 33.333 0.45 0.00 39.24 2.17
52 53 6.842437 TGACGGGATTAATTTCCAAATTCA 57.158 33.333 0.45 0.00 39.24 2.57
53 54 6.862209 TGACGGGATTAATTTCCAAATTCAG 58.138 36.000 0.45 0.00 39.24 3.02
54 55 6.435904 TGACGGGATTAATTTCCAAATTCAGT 59.564 34.615 0.45 0.00 39.24 3.41
55 56 7.039363 TGACGGGATTAATTTCCAAATTCAGTT 60.039 33.333 0.45 0.00 39.24 3.16
56 57 7.676004 ACGGGATTAATTTCCAAATTCAGTTT 58.324 30.769 0.45 0.00 39.24 2.66
57 58 7.817478 ACGGGATTAATTTCCAAATTCAGTTTC 59.183 33.333 0.45 0.00 39.24 2.78
58 59 7.009174 CGGGATTAATTTCCAAATTCAGTTTCG 59.991 37.037 0.45 0.00 39.24 3.46
59 60 7.817478 GGGATTAATTTCCAAATTCAGTTTCGT 59.183 33.333 0.45 0.00 39.24 3.85
60 61 9.203421 GGATTAATTTCCAAATTCAGTTTCGTT 57.797 29.630 0.45 0.00 39.24 3.85
81 82 2.953640 TTTAGTAAAACCTGTGCGCG 57.046 45.000 0.00 0.00 0.00 6.86
82 83 0.513820 TTAGTAAAACCTGTGCGCGC 59.486 50.000 27.26 27.26 0.00 6.86
83 84 0.320073 TAGTAAAACCTGTGCGCGCT 60.320 50.000 33.29 11.88 0.00 5.92
84 85 1.154469 GTAAAACCTGTGCGCGCTC 60.154 57.895 33.29 29.03 0.00 5.03
85 86 1.301401 TAAAACCTGTGCGCGCTCT 60.301 52.632 33.29 13.85 0.00 4.09
86 87 1.289109 TAAAACCTGTGCGCGCTCTC 61.289 55.000 33.29 21.59 0.00 3.20
89 90 4.749310 CCTGTGCGCGCTCTCCTT 62.749 66.667 33.29 0.00 0.00 3.36
90 91 3.184683 CTGTGCGCGCTCTCCTTC 61.185 66.667 33.29 13.31 0.00 3.46
91 92 3.921767 CTGTGCGCGCTCTCCTTCA 62.922 63.158 33.29 16.79 0.00 3.02
92 93 2.738521 GTGCGCGCTCTCCTTCAA 60.739 61.111 33.29 5.03 0.00 2.69
93 94 2.103042 GTGCGCGCTCTCCTTCAAT 61.103 57.895 33.29 0.00 0.00 2.57
94 95 1.811266 TGCGCGCTCTCCTTCAATC 60.811 57.895 33.29 0.00 0.00 2.67
95 96 1.520342 GCGCGCTCTCCTTCAATCT 60.520 57.895 26.67 0.00 0.00 2.40
96 97 1.486644 GCGCGCTCTCCTTCAATCTC 61.487 60.000 26.67 0.00 0.00 2.75
97 98 0.179127 CGCGCTCTCCTTCAATCTCA 60.179 55.000 5.56 0.00 0.00 3.27
98 99 1.737029 CGCGCTCTCCTTCAATCTCAA 60.737 52.381 5.56 0.00 0.00 3.02
99 100 1.663135 GCGCTCTCCTTCAATCTCAAC 59.337 52.381 0.00 0.00 0.00 3.18
100 101 2.275318 CGCTCTCCTTCAATCTCAACC 58.725 52.381 0.00 0.00 0.00 3.77
101 102 2.093764 CGCTCTCCTTCAATCTCAACCT 60.094 50.000 0.00 0.00 0.00 3.50
102 103 3.269178 GCTCTCCTTCAATCTCAACCTG 58.731 50.000 0.00 0.00 0.00 4.00
103 104 3.269178 CTCTCCTTCAATCTCAACCTGC 58.731 50.000 0.00 0.00 0.00 4.85
104 105 2.026822 TCTCCTTCAATCTCAACCTGCC 60.027 50.000 0.00 0.00 0.00 4.85
105 106 1.988107 TCCTTCAATCTCAACCTGCCT 59.012 47.619 0.00 0.00 0.00 4.75
106 107 3.181329 TCCTTCAATCTCAACCTGCCTA 58.819 45.455 0.00 0.00 0.00 3.93
107 108 3.587061 TCCTTCAATCTCAACCTGCCTAA 59.413 43.478 0.00 0.00 0.00 2.69
108 109 4.042809 TCCTTCAATCTCAACCTGCCTAAA 59.957 41.667 0.00 0.00 0.00 1.85
109 110 4.952335 CCTTCAATCTCAACCTGCCTAAAT 59.048 41.667 0.00 0.00 0.00 1.40
110 111 5.067023 CCTTCAATCTCAACCTGCCTAAATC 59.933 44.000 0.00 0.00 0.00 2.17
111 112 4.191544 TCAATCTCAACCTGCCTAAATCG 58.808 43.478 0.00 0.00 0.00 3.34
112 113 2.024176 TCTCAACCTGCCTAAATCGC 57.976 50.000 0.00 0.00 0.00 4.58
113 114 1.277842 TCTCAACCTGCCTAAATCGCA 59.722 47.619 0.00 0.00 34.41 5.10
114 115 2.083774 CTCAACCTGCCTAAATCGCAA 58.916 47.619 0.00 0.00 35.40 4.85
115 116 2.487762 CTCAACCTGCCTAAATCGCAAA 59.512 45.455 0.00 0.00 35.40 3.68
116 117 2.487762 TCAACCTGCCTAAATCGCAAAG 59.512 45.455 0.00 0.00 35.40 2.77
117 118 0.811281 ACCTGCCTAAATCGCAAAGC 59.189 50.000 0.00 0.00 35.40 3.51
118 119 1.098050 CCTGCCTAAATCGCAAAGCT 58.902 50.000 0.00 0.00 35.40 3.74
119 120 1.474077 CCTGCCTAAATCGCAAAGCTT 59.526 47.619 0.00 0.00 35.40 3.74
120 121 2.094545 CCTGCCTAAATCGCAAAGCTTT 60.095 45.455 5.69 5.69 35.40 3.51
121 122 3.578688 CTGCCTAAATCGCAAAGCTTTT 58.421 40.909 9.53 0.00 35.40 2.27
122 123 3.988819 TGCCTAAATCGCAAAGCTTTTT 58.011 36.364 9.53 3.55 32.05 1.94
123 124 3.987220 TGCCTAAATCGCAAAGCTTTTTC 59.013 39.130 9.53 3.53 32.05 2.29
124 125 4.237724 GCCTAAATCGCAAAGCTTTTTCT 58.762 39.130 9.53 0.00 0.00 2.52
125 126 4.686091 GCCTAAATCGCAAAGCTTTTTCTT 59.314 37.500 9.53 1.87 0.00 2.52
126 127 5.861787 GCCTAAATCGCAAAGCTTTTTCTTA 59.138 36.000 9.53 2.92 0.00 2.10
127 128 6.033937 GCCTAAATCGCAAAGCTTTTTCTTAG 59.966 38.462 9.53 11.38 0.00 2.18
128 129 6.528072 CCTAAATCGCAAAGCTTTTTCTTAGG 59.472 38.462 9.53 15.73 0.00 2.69
129 130 3.282831 TCGCAAAGCTTTTTCTTAGGC 57.717 42.857 9.53 7.15 0.00 3.93
130 131 1.978782 CGCAAAGCTTTTTCTTAGGCG 59.021 47.619 19.05 19.05 40.70 5.52
131 132 1.721389 GCAAAGCTTTTTCTTAGGCGC 59.279 47.619 9.53 0.00 0.00 6.53
132 133 2.608016 GCAAAGCTTTTTCTTAGGCGCT 60.608 45.455 9.53 0.00 0.00 5.92
133 134 3.237628 CAAAGCTTTTTCTTAGGCGCTC 58.762 45.455 9.53 0.00 0.00 5.03
134 135 2.481289 AGCTTTTTCTTAGGCGCTCT 57.519 45.000 7.64 5.38 0.00 4.09
135 136 3.611766 AGCTTTTTCTTAGGCGCTCTA 57.388 42.857 7.64 4.23 0.00 2.43
136 137 4.143986 AGCTTTTTCTTAGGCGCTCTAT 57.856 40.909 7.64 0.00 0.00 1.98
137 138 3.873952 AGCTTTTTCTTAGGCGCTCTATG 59.126 43.478 7.64 9.60 0.00 2.23
138 139 3.547014 GCTTTTTCTTAGGCGCTCTATGC 60.547 47.826 7.64 0.00 38.57 3.14
139 140 2.979814 TTTCTTAGGCGCTCTATGCA 57.020 45.000 7.64 0.00 43.06 3.96
140 141 2.225068 TTCTTAGGCGCTCTATGCAC 57.775 50.000 7.64 0.00 43.06 4.57
141 142 0.389391 TCTTAGGCGCTCTATGCACC 59.611 55.000 7.64 0.00 43.89 5.01
144 145 2.590007 GGCGCTCTATGCACCTGG 60.590 66.667 7.64 0.00 40.56 4.45
145 146 2.501128 GCGCTCTATGCACCTGGA 59.499 61.111 0.00 0.00 43.06 3.86
146 147 1.884926 GCGCTCTATGCACCTGGAC 60.885 63.158 0.00 0.00 43.06 4.02
147 148 1.589993 CGCTCTATGCACCTGGACG 60.590 63.158 0.00 0.00 43.06 4.79
148 149 1.227380 GCTCTATGCACCTGGACGG 60.227 63.158 0.00 0.00 42.31 4.79
149 150 1.676678 GCTCTATGCACCTGGACGGA 61.677 60.000 0.00 0.00 42.31 4.69
150 151 0.387202 CTCTATGCACCTGGACGGAG 59.613 60.000 0.00 0.00 36.31 4.63
151 152 1.043116 TCTATGCACCTGGACGGAGG 61.043 60.000 0.00 0.00 39.28 4.30
152 153 2.032860 CTATGCACCTGGACGGAGGG 62.033 65.000 0.00 0.00 37.45 4.30
153 154 2.523740 TATGCACCTGGACGGAGGGA 62.524 60.000 0.00 0.00 37.45 4.20
154 155 3.775654 GCACCTGGACGGAGGGAG 61.776 72.222 0.00 0.00 37.45 4.30
155 156 2.283966 CACCTGGACGGAGGGAGT 60.284 66.667 0.00 0.00 37.45 3.85
156 157 1.000019 CACCTGGACGGAGGGAGTA 60.000 63.158 0.00 0.00 37.45 2.59
157 158 1.000107 ACCTGGACGGAGGGAGTAC 60.000 63.158 0.00 0.00 37.45 2.73
158 159 1.306970 CCTGGACGGAGGGAGTACT 59.693 63.158 0.00 0.00 33.16 2.73
159 160 0.324460 CCTGGACGGAGGGAGTACTT 60.324 60.000 0.00 0.00 33.16 2.24
160 161 1.104630 CTGGACGGAGGGAGTACTTC 58.895 60.000 0.00 0.00 0.00 3.01
161 162 0.702902 TGGACGGAGGGAGTACTTCT 59.297 55.000 0.01 0.06 0.00 2.85
162 163 1.076677 TGGACGGAGGGAGTACTTCTT 59.923 52.381 0.01 0.00 0.00 2.52
163 164 2.177734 GGACGGAGGGAGTACTTCTTT 58.822 52.381 0.01 0.00 0.00 2.52
164 165 2.094130 GGACGGAGGGAGTACTTCTTTG 60.094 54.545 0.01 0.00 0.00 2.77
165 166 2.561858 GACGGAGGGAGTACTTCTTTGT 59.438 50.000 0.01 0.00 0.00 2.83
166 167 3.760684 GACGGAGGGAGTACTTCTTTGTA 59.239 47.826 0.01 0.00 0.00 2.41
167 168 3.762823 ACGGAGGGAGTACTTCTTTGTAG 59.237 47.826 0.01 0.00 0.00 2.74
168 169 3.762823 CGGAGGGAGTACTTCTTTGTAGT 59.237 47.826 0.01 0.00 0.00 2.73
169 170 4.380655 CGGAGGGAGTACTTCTTTGTAGTG 60.381 50.000 0.01 0.00 0.00 2.74
170 171 4.081586 GGAGGGAGTACTTCTTTGTAGTGG 60.082 50.000 0.01 0.00 0.00 4.00
171 172 3.261137 AGGGAGTACTTCTTTGTAGTGGC 59.739 47.826 0.01 0.00 0.00 5.01
172 173 3.007614 GGGAGTACTTCTTTGTAGTGGCA 59.992 47.826 0.01 0.00 0.00 4.92
182 183 4.218200 TCTTTGTAGTGGCATGATGTTTGG 59.782 41.667 0.00 0.00 0.00 3.28
210 211 9.278734 GAAATGATAGAATGTTTTTCTCGGTTC 57.721 33.333 0.00 0.00 0.00 3.62
288 290 2.434331 CCTTTCTTCGGCCCACCA 59.566 61.111 0.00 0.00 34.57 4.17
312 314 3.314331 CGGAGCCTGTCTGGTGGT 61.314 66.667 0.00 0.00 38.35 4.16
313 315 2.665603 GGAGCCTGTCTGGTGGTC 59.334 66.667 0.00 0.00 38.35 4.02
314 316 1.915769 GGAGCCTGTCTGGTGGTCT 60.916 63.158 0.00 0.00 38.35 3.85
315 317 0.614979 GGAGCCTGTCTGGTGGTCTA 60.615 60.000 0.00 0.00 38.35 2.59
316 318 0.820871 GAGCCTGTCTGGTGGTCTAG 59.179 60.000 0.00 0.00 38.35 2.43
317 319 0.115349 AGCCTGTCTGGTGGTCTAGT 59.885 55.000 0.00 0.00 38.35 2.57
318 320 0.533032 GCCTGTCTGGTGGTCTAGTC 59.467 60.000 0.00 0.00 38.35 2.59
319 321 0.811915 CCTGTCTGGTGGTCTAGTCG 59.188 60.000 0.00 0.00 0.00 4.18
320 322 0.171455 CTGTCTGGTGGTCTAGTCGC 59.829 60.000 0.00 0.00 0.00 5.19
321 323 1.136984 GTCTGGTGGTCTAGTCGCG 59.863 63.158 0.00 0.00 0.00 5.87
322 324 2.044555 TCTGGTGGTCTAGTCGCGG 61.045 63.158 6.13 0.00 0.00 6.46
323 325 3.701604 CTGGTGGTCTAGTCGCGGC 62.702 68.421 0.21 0.21 0.00 6.53
324 326 4.849329 GGTGGTCTAGTCGCGGCG 62.849 72.222 17.70 17.70 0.00 6.46
325 327 4.849329 GTGGTCTAGTCGCGGCGG 62.849 72.222 23.46 6.26 0.00 6.13
327 329 4.549516 GGTCTAGTCGCGGCGGTC 62.550 72.222 23.46 15.55 0.00 4.79
328 330 4.883300 GTCTAGTCGCGGCGGTCG 62.883 72.222 23.46 4.52 42.76 4.79
447 456 3.760035 CGTCCTCCTCCCCACACG 61.760 72.222 0.00 0.00 0.00 4.49
473 482 2.203938 TCTCCACCTCCACCACCC 60.204 66.667 0.00 0.00 0.00 4.61
1094 1362 4.078516 GCCACCTTCGCCTACCGT 62.079 66.667 0.00 0.00 38.35 4.83
1260 1528 1.448119 CCTGGACTATCTGCGCGAGA 61.448 60.000 12.10 10.76 34.25 4.04
1415 1683 0.110486 GGGAGGAGGTGCACAAGAAA 59.890 55.000 20.43 0.00 0.00 2.52
1556 1824 5.598005 CAGAGATAGGATCCTCTCAGTGTTT 59.402 44.000 25.27 8.44 40.31 2.83
1612 1880 0.883814 AGCTCAGTTCACAGTGCAGC 60.884 55.000 0.00 0.00 31.60 5.25
1721 1989 4.228210 AGGGCAAGGAAGATGTATCTGAAA 59.772 41.667 0.00 0.00 37.19 2.69
1727 1995 7.094205 GCAAGGAAGATGTATCTGAAAAGGAAA 60.094 37.037 0.00 0.00 37.19 3.13
1904 2172 1.484444 GGGCAGAGGAGACAGTGGTT 61.484 60.000 0.00 0.00 0.00 3.67
2004 2272 1.634973 TGAGGGATCAGTTGCCATCAA 59.365 47.619 0.00 0.00 41.46 2.57
2024 2292 3.914426 ACATTGGTGGACTCCTATGAC 57.086 47.619 17.36 0.00 41.02 3.06
2051 2319 2.093128 ACAGGAAACACTCGACAGGTTT 60.093 45.455 4.53 4.53 37.44 3.27
2132 2400 5.242838 GGAGGACGAGAGACAATATGAGAAT 59.757 44.000 0.00 0.00 0.00 2.40
2681 2949 3.863424 GGATACGTCTTTTGCAGAATCGA 59.137 43.478 16.91 0.00 31.28 3.59
2880 3153 4.870123 AAAACAACTTGCATGATGCCTA 57.130 36.364 15.70 1.95 44.23 3.93
3084 3376 3.120199 GGTGCTACATGTCACAACATCAC 60.120 47.826 16.82 5.09 44.41 3.06
3285 3939 6.322969 TGTCTAGGTTTGAGACTAAGTTGACA 59.677 38.462 4.57 0.00 43.19 3.58
3289 3943 7.304497 AGGTTTGAGACTAAGTTGACACTAT 57.696 36.000 0.00 0.00 30.68 2.12
3346 4000 5.071653 AGGTTTTGTTTGCCTATGATTTGGT 59.928 36.000 0.00 0.00 0.00 3.67
3575 4244 0.106519 ACACCATATGCTTCCCCTGC 60.107 55.000 0.00 0.00 0.00 4.85
3576 4245 1.149174 ACCATATGCTTCCCCTGCG 59.851 57.895 0.00 0.00 0.00 5.18
3588 4257 3.420300 TCCCCTGCGTGTGTTTATAAA 57.580 42.857 0.00 0.00 0.00 1.40
3595 4264 8.573035 CCCCTGCGTGTGTTTATAAATTTATAT 58.427 33.333 16.71 0.00 0.00 0.86
3675 4344 8.027771 TCTCTTAATTAGTCGGTCTGAAACTTC 58.972 37.037 0.00 0.00 0.00 3.01
3747 4416 3.636300 TGGCTTTGCTGTGTAATTTGACT 59.364 39.130 0.00 0.00 0.00 3.41
3753 4422 6.968131 TTGCTGTGTAATTTGACTAGCTAG 57.032 37.500 19.44 19.44 33.89 3.42
3770 4439 0.797579 TAGTTCCCCCTGTTCCTCCT 59.202 55.000 0.00 0.00 0.00 3.69
3854 5326 5.241506 TGTTTCAGGAGGCTTTAAGAATGTG 59.758 40.000 0.00 0.00 0.00 3.21
3864 5336 7.154656 AGGCTTTAAGAATGTGAAATTTGGTC 58.845 34.615 0.00 0.00 0.00 4.02
3867 5339 7.148967 GCTTTAAGAATGTGAAATTTGGTCGAC 60.149 37.037 7.13 7.13 0.00 4.20
3898 5370 5.903764 TGTTTCGGCAATTTGAATTTGAG 57.096 34.783 0.00 0.00 0.00 3.02
3916 5388 4.263018 TGAGCTATTCTCCAATCCATCG 57.737 45.455 0.00 0.00 41.18 3.84
3917 5389 3.897505 TGAGCTATTCTCCAATCCATCGA 59.102 43.478 0.00 0.00 41.18 3.59
3918 5390 4.529769 TGAGCTATTCTCCAATCCATCGAT 59.470 41.667 0.00 0.00 41.18 3.59
3919 5391 5.083533 AGCTATTCTCCAATCCATCGATC 57.916 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.451783 GCCGTTTCAGCTAACCCATG 59.548 55.000 0.00 0.00 0.00 3.66
1 2 0.679960 GGCCGTTTCAGCTAACCCAT 60.680 55.000 0.00 0.00 0.00 4.00
2 3 1.302993 GGCCGTTTCAGCTAACCCA 60.303 57.895 0.00 0.00 0.00 4.51
3 4 0.891904 TTGGCCGTTTCAGCTAACCC 60.892 55.000 0.00 0.00 0.00 4.11
4 5 0.240145 GTTGGCCGTTTCAGCTAACC 59.760 55.000 0.00 0.00 43.56 2.85
5 6 3.767287 GTTGGCCGTTTCAGCTAAC 57.233 52.632 0.00 0.00 43.10 2.34
6 7 0.948678 GTGTTGGCCGTTTCAGCTAA 59.051 50.000 0.00 0.00 0.00 3.09
7 8 0.107831 AGTGTTGGCCGTTTCAGCTA 59.892 50.000 0.00 0.00 0.00 3.32
8 9 0.107831 TAGTGTTGGCCGTTTCAGCT 59.892 50.000 0.00 0.00 0.00 4.24
9 10 0.948678 TTAGTGTTGGCCGTTTCAGC 59.051 50.000 0.00 0.00 0.00 4.26
10 11 2.811431 TCATTAGTGTTGGCCGTTTCAG 59.189 45.455 0.00 0.00 0.00 3.02
11 12 2.550606 GTCATTAGTGTTGGCCGTTTCA 59.449 45.455 0.00 0.00 0.00 2.69
12 13 2.412325 CGTCATTAGTGTTGGCCGTTTC 60.412 50.000 0.00 0.00 0.00 2.78
13 14 1.533731 CGTCATTAGTGTTGGCCGTTT 59.466 47.619 0.00 0.00 0.00 3.60
14 15 1.153353 CGTCATTAGTGTTGGCCGTT 58.847 50.000 0.00 0.00 0.00 4.44
15 16 0.672401 CCGTCATTAGTGTTGGCCGT 60.672 55.000 0.00 0.00 0.00 5.68
16 17 1.366111 CCCGTCATTAGTGTTGGCCG 61.366 60.000 0.00 0.00 0.00 6.13
17 18 0.035820 TCCCGTCATTAGTGTTGGCC 60.036 55.000 0.00 0.00 0.00 5.36
18 19 2.038387 ATCCCGTCATTAGTGTTGGC 57.962 50.000 0.00 0.00 0.00 4.52
19 20 6.693315 AATTAATCCCGTCATTAGTGTTGG 57.307 37.500 0.00 0.00 0.00 3.77
20 21 7.148154 TGGAAATTAATCCCGTCATTAGTGTTG 60.148 37.037 0.00 0.00 38.82 3.33
21 22 6.887545 TGGAAATTAATCCCGTCATTAGTGTT 59.112 34.615 0.00 0.00 38.82 3.32
22 23 6.419791 TGGAAATTAATCCCGTCATTAGTGT 58.580 36.000 0.00 0.00 38.82 3.55
23 24 6.935741 TGGAAATTAATCCCGTCATTAGTG 57.064 37.500 0.00 0.00 38.82 2.74
24 25 7.948034 TTTGGAAATTAATCCCGTCATTAGT 57.052 32.000 0.00 0.00 38.82 2.24
25 26 9.463443 GAATTTGGAAATTAATCCCGTCATTAG 57.537 33.333 0.00 0.00 38.64 1.73
26 27 8.972127 TGAATTTGGAAATTAATCCCGTCATTA 58.028 29.630 0.00 0.00 38.64 1.90
27 28 7.846066 TGAATTTGGAAATTAATCCCGTCATT 58.154 30.769 0.00 0.00 38.64 2.57
28 29 7.124147 ACTGAATTTGGAAATTAATCCCGTCAT 59.876 33.333 0.00 0.00 38.64 3.06
29 30 6.435904 ACTGAATTTGGAAATTAATCCCGTCA 59.564 34.615 0.00 0.00 38.64 4.35
30 31 6.863275 ACTGAATTTGGAAATTAATCCCGTC 58.137 36.000 0.00 0.00 38.64 4.79
31 32 6.850752 ACTGAATTTGGAAATTAATCCCGT 57.149 33.333 0.00 0.00 38.64 5.28
32 33 7.009174 CGAAACTGAATTTGGAAATTAATCCCG 59.991 37.037 0.00 0.00 38.64 5.14
33 34 7.817478 ACGAAACTGAATTTGGAAATTAATCCC 59.183 33.333 0.00 0.00 38.64 3.85
34 35 8.757164 ACGAAACTGAATTTGGAAATTAATCC 57.243 30.769 0.00 0.00 38.64 3.01
60 61 3.619729 CGCGCACAGGTTTTACTAAAAA 58.380 40.909 8.75 0.00 32.15 1.94
61 62 2.602694 GCGCGCACAGGTTTTACTAAAA 60.603 45.455 29.10 0.00 0.00 1.52
62 63 1.069771 GCGCGCACAGGTTTTACTAAA 60.070 47.619 29.10 0.00 0.00 1.85
63 64 0.513820 GCGCGCACAGGTTTTACTAA 59.486 50.000 29.10 0.00 0.00 2.24
64 65 0.320073 AGCGCGCACAGGTTTTACTA 60.320 50.000 35.10 0.00 0.00 1.82
65 66 1.566018 GAGCGCGCACAGGTTTTACT 61.566 55.000 35.10 7.44 0.00 2.24
66 67 1.154469 GAGCGCGCACAGGTTTTAC 60.154 57.895 35.10 6.95 0.00 2.01
67 68 1.289109 GAGAGCGCGCACAGGTTTTA 61.289 55.000 35.10 0.00 0.00 1.52
68 69 2.591715 AGAGCGCGCACAGGTTTT 60.592 55.556 35.10 9.89 0.00 2.43
69 70 3.044305 GAGAGCGCGCACAGGTTT 61.044 61.111 35.10 10.81 0.00 3.27
72 73 4.749310 AAGGAGAGCGCGCACAGG 62.749 66.667 35.10 0.00 0.00 4.00
73 74 3.184683 GAAGGAGAGCGCGCACAG 61.185 66.667 35.10 0.00 0.00 3.66
74 75 2.786539 ATTGAAGGAGAGCGCGCACA 62.787 55.000 35.10 17.00 0.00 4.57
75 76 2.029904 GATTGAAGGAGAGCGCGCAC 62.030 60.000 35.10 28.25 0.00 5.34
76 77 1.811266 GATTGAAGGAGAGCGCGCA 60.811 57.895 35.10 9.50 0.00 6.09
77 78 1.486644 GAGATTGAAGGAGAGCGCGC 61.487 60.000 26.66 26.66 0.00 6.86
78 79 0.179127 TGAGATTGAAGGAGAGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
79 80 1.663135 GTTGAGATTGAAGGAGAGCGC 59.337 52.381 0.00 0.00 0.00 5.92
80 81 2.093764 AGGTTGAGATTGAAGGAGAGCG 60.094 50.000 0.00 0.00 0.00 5.03
81 82 3.269178 CAGGTTGAGATTGAAGGAGAGC 58.731 50.000 0.00 0.00 0.00 4.09
82 83 3.269178 GCAGGTTGAGATTGAAGGAGAG 58.731 50.000 0.00 0.00 0.00 3.20
83 84 2.026822 GGCAGGTTGAGATTGAAGGAGA 60.027 50.000 0.00 0.00 0.00 3.71
84 85 2.026449 AGGCAGGTTGAGATTGAAGGAG 60.026 50.000 0.00 0.00 0.00 3.69
85 86 1.988107 AGGCAGGTTGAGATTGAAGGA 59.012 47.619 0.00 0.00 0.00 3.36
86 87 2.503895 AGGCAGGTTGAGATTGAAGG 57.496 50.000 0.00 0.00 0.00 3.46
87 88 5.220739 CGATTTAGGCAGGTTGAGATTGAAG 60.221 44.000 0.00 0.00 0.00 3.02
88 89 4.635765 CGATTTAGGCAGGTTGAGATTGAA 59.364 41.667 0.00 0.00 0.00 2.69
89 90 4.191544 CGATTTAGGCAGGTTGAGATTGA 58.808 43.478 0.00 0.00 0.00 2.57
90 91 3.242870 GCGATTTAGGCAGGTTGAGATTG 60.243 47.826 0.00 0.00 0.00 2.67
91 92 2.945668 GCGATTTAGGCAGGTTGAGATT 59.054 45.455 0.00 0.00 0.00 2.40
92 93 2.092968 TGCGATTTAGGCAGGTTGAGAT 60.093 45.455 0.00 0.00 35.04 2.75
93 94 1.277842 TGCGATTTAGGCAGGTTGAGA 59.722 47.619 0.00 0.00 35.04 3.27
94 95 1.737838 TGCGATTTAGGCAGGTTGAG 58.262 50.000 0.00 0.00 35.04 3.02
95 96 2.192664 TTGCGATTTAGGCAGGTTGA 57.807 45.000 0.00 0.00 42.12 3.18
96 97 2.867429 CTTTGCGATTTAGGCAGGTTG 58.133 47.619 0.00 0.00 42.12 3.77
97 98 1.202348 GCTTTGCGATTTAGGCAGGTT 59.798 47.619 0.00 0.00 42.12 3.50
98 99 0.811281 GCTTTGCGATTTAGGCAGGT 59.189 50.000 0.00 0.00 42.12 4.00
99 100 1.098050 AGCTTTGCGATTTAGGCAGG 58.902 50.000 0.00 0.00 42.12 4.85
100 101 2.927553 AAGCTTTGCGATTTAGGCAG 57.072 45.000 0.00 0.00 42.12 4.85
101 102 3.658757 AAAAGCTTTGCGATTTAGGCA 57.341 38.095 13.54 0.00 38.93 4.75
102 103 4.237724 AGAAAAAGCTTTGCGATTTAGGC 58.762 39.130 13.54 0.00 29.68 3.93
103 104 6.528072 CCTAAGAAAAAGCTTTGCGATTTAGG 59.472 38.462 13.54 18.81 29.68 2.69
104 105 6.033937 GCCTAAGAAAAAGCTTTGCGATTTAG 59.966 38.462 13.54 14.72 29.68 1.85
105 106 5.861787 GCCTAAGAAAAAGCTTTGCGATTTA 59.138 36.000 13.54 7.01 29.68 1.40
106 107 4.686091 GCCTAAGAAAAAGCTTTGCGATTT 59.314 37.500 13.54 2.24 31.41 2.17
107 108 4.237724 GCCTAAGAAAAAGCTTTGCGATT 58.762 39.130 13.54 2.66 0.00 3.34
108 109 3.670627 CGCCTAAGAAAAAGCTTTGCGAT 60.671 43.478 24.93 11.15 43.98 4.58
109 110 2.350388 CGCCTAAGAAAAAGCTTTGCGA 60.350 45.455 24.93 9.65 43.98 5.10
110 111 1.978782 CGCCTAAGAAAAAGCTTTGCG 59.021 47.619 19.05 19.05 39.62 4.85
111 112 1.721389 GCGCCTAAGAAAAAGCTTTGC 59.279 47.619 13.54 8.84 0.00 3.68
112 113 3.057946 AGAGCGCCTAAGAAAAAGCTTTG 60.058 43.478 13.54 0.00 34.85 2.77
113 114 3.149981 AGAGCGCCTAAGAAAAAGCTTT 58.850 40.909 5.69 5.69 34.85 3.51
114 115 2.784347 AGAGCGCCTAAGAAAAAGCTT 58.216 42.857 2.29 0.00 34.85 3.74
115 116 2.481289 AGAGCGCCTAAGAAAAAGCT 57.519 45.000 2.29 0.00 37.69 3.74
116 117 3.547014 GCATAGAGCGCCTAAGAAAAAGC 60.547 47.826 2.29 0.00 0.00 3.51
117 118 4.202578 GCATAGAGCGCCTAAGAAAAAG 57.797 45.455 2.29 0.00 0.00 2.27
130 131 1.227380 CCGTCCAGGTGCATAGAGC 60.227 63.158 0.00 0.00 45.96 4.09
131 132 0.387202 CTCCGTCCAGGTGCATAGAG 59.613 60.000 0.00 0.00 41.99 2.43
132 133 1.043116 CCTCCGTCCAGGTGCATAGA 61.043 60.000 0.00 0.00 41.99 1.98
133 134 1.443407 CCTCCGTCCAGGTGCATAG 59.557 63.158 0.00 0.00 41.99 2.23
134 135 2.063979 CCCTCCGTCCAGGTGCATA 61.064 63.158 0.00 0.00 41.99 3.14
135 136 3.402681 CCCTCCGTCCAGGTGCAT 61.403 66.667 0.00 0.00 41.99 3.96
136 137 4.631740 TCCCTCCGTCCAGGTGCA 62.632 66.667 0.00 0.00 41.99 4.57
137 138 3.775654 CTCCCTCCGTCCAGGTGC 61.776 72.222 0.00 0.00 41.99 5.01
138 139 1.000019 TACTCCCTCCGTCCAGGTG 60.000 63.158 0.00 0.00 41.99 4.00
139 140 1.000107 GTACTCCCTCCGTCCAGGT 60.000 63.158 0.00 0.00 41.99 4.00
140 141 0.324460 AAGTACTCCCTCCGTCCAGG 60.324 60.000 0.00 0.00 42.97 4.45
141 142 1.104630 GAAGTACTCCCTCCGTCCAG 58.895 60.000 0.00 0.00 0.00 3.86
142 143 0.702902 AGAAGTACTCCCTCCGTCCA 59.297 55.000 0.00 0.00 0.00 4.02
143 144 1.849977 AAGAAGTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
144 145 2.561858 ACAAAGAAGTACTCCCTCCGTC 59.438 50.000 0.00 0.00 0.00 4.79
145 146 2.606378 ACAAAGAAGTACTCCCTCCGT 58.394 47.619 0.00 0.00 0.00 4.69
146 147 3.762823 ACTACAAAGAAGTACTCCCTCCG 59.237 47.826 0.00 0.00 0.00 4.63
147 148 4.081586 CCACTACAAAGAAGTACTCCCTCC 60.082 50.000 0.00 0.00 0.00 4.30
148 149 4.621038 GCCACTACAAAGAAGTACTCCCTC 60.621 50.000 0.00 0.00 0.00 4.30
149 150 3.261137 GCCACTACAAAGAAGTACTCCCT 59.739 47.826 0.00 0.00 0.00 4.20
150 151 3.007614 TGCCACTACAAAGAAGTACTCCC 59.992 47.826 0.00 0.00 0.00 4.30
151 152 4.267349 TGCCACTACAAAGAAGTACTCC 57.733 45.455 0.00 0.00 0.00 3.85
152 153 5.479306 TCATGCCACTACAAAGAAGTACTC 58.521 41.667 0.00 0.00 0.00 2.59
153 154 5.483685 TCATGCCACTACAAAGAAGTACT 57.516 39.130 0.00 0.00 0.00 2.73
154 155 5.643777 ACATCATGCCACTACAAAGAAGTAC 59.356 40.000 0.00 0.00 0.00 2.73
155 156 5.804639 ACATCATGCCACTACAAAGAAGTA 58.195 37.500 0.00 0.00 0.00 2.24
156 157 4.655963 ACATCATGCCACTACAAAGAAGT 58.344 39.130 0.00 0.00 0.00 3.01
157 158 5.633830 AACATCATGCCACTACAAAGAAG 57.366 39.130 0.00 0.00 0.00 2.85
158 159 5.278907 CCAAACATCATGCCACTACAAAGAA 60.279 40.000 0.00 0.00 0.00 2.52
159 160 4.218200 CCAAACATCATGCCACTACAAAGA 59.782 41.667 0.00 0.00 0.00 2.52
160 161 4.022068 ACCAAACATCATGCCACTACAAAG 60.022 41.667 0.00 0.00 0.00 2.77
161 162 3.894427 ACCAAACATCATGCCACTACAAA 59.106 39.130 0.00 0.00 0.00 2.83
162 163 3.255395 CACCAAACATCATGCCACTACAA 59.745 43.478 0.00 0.00 0.00 2.41
163 164 2.819019 CACCAAACATCATGCCACTACA 59.181 45.455 0.00 0.00 0.00 2.74
164 165 3.081061 TCACCAAACATCATGCCACTAC 58.919 45.455 0.00 0.00 0.00 2.73
165 166 3.431673 TCACCAAACATCATGCCACTA 57.568 42.857 0.00 0.00 0.00 2.74
166 167 2.291209 TCACCAAACATCATGCCACT 57.709 45.000 0.00 0.00 0.00 4.00
167 168 3.383620 TTTCACCAAACATCATGCCAC 57.616 42.857 0.00 0.00 0.00 5.01
168 169 3.577415 TCATTTCACCAAACATCATGCCA 59.423 39.130 0.00 0.00 0.00 4.92
169 170 4.191033 TCATTTCACCAAACATCATGCC 57.809 40.909 0.00 0.00 0.00 4.40
170 171 6.798482 TCTATCATTTCACCAAACATCATGC 58.202 36.000 0.00 0.00 0.00 4.06
171 172 9.244799 CATTCTATCATTTCACCAAACATCATG 57.755 33.333 0.00 0.00 0.00 3.07
172 173 8.974238 ACATTCTATCATTTCACCAAACATCAT 58.026 29.630 0.00 0.00 0.00 2.45
182 183 8.237267 ACCGAGAAAAACATTCTATCATTTCAC 58.763 33.333 0.00 0.00 31.06 3.18
210 211 6.096141 ACAAATGGCCCAAAAAGGTTAAAAAG 59.904 34.615 0.00 0.00 34.66 2.27
298 300 0.115349 ACTAGACCACCAGACAGGCT 59.885 55.000 0.00 0.00 43.14 4.58
300 302 0.811915 CGACTAGACCACCAGACAGG 59.188 60.000 0.00 0.00 45.67 4.00
301 303 0.171455 GCGACTAGACCACCAGACAG 59.829 60.000 0.00 0.00 0.00 3.51
302 304 1.583495 CGCGACTAGACCACCAGACA 61.583 60.000 0.00 0.00 0.00 3.41
304 306 2.044555 CCGCGACTAGACCACCAGA 61.045 63.158 8.23 0.00 0.00 3.86
305 307 2.490217 CCGCGACTAGACCACCAG 59.510 66.667 8.23 0.00 0.00 4.00
306 308 3.755628 GCCGCGACTAGACCACCA 61.756 66.667 8.23 0.00 0.00 4.17
307 309 4.849329 CGCCGCGACTAGACCACC 62.849 72.222 8.23 0.00 0.00 4.61
308 310 4.849329 CCGCCGCGACTAGACCAC 62.849 72.222 15.93 0.00 0.00 4.16
310 312 4.549516 GACCGCCGCGACTAGACC 62.550 72.222 15.93 0.00 0.00 3.85
311 313 4.883300 CGACCGCCGCGACTAGAC 62.883 72.222 15.93 0.00 0.00 2.59
329 331 0.039165 GGGAGGAAAGCGCAAGTTTG 60.039 55.000 11.47 0.00 41.07 2.93
1260 1528 1.043816 ATCGCATCGGAGAGGAACAT 58.956 50.000 0.00 0.00 43.16 2.71
1347 1615 6.014840 ACAGGATCAAAGAAAATGTTCAGCAT 60.015 34.615 0.00 0.00 40.03 3.79
1358 1626 6.126940 CCTCTCTATCCACAGGATCAAAGAAA 60.127 42.308 1.05 0.00 42.11 2.52
1415 1683 5.749462 CTGTCATCCTTAACTCTGGGATTT 58.251 41.667 0.00 0.00 37.72 2.17
1556 1824 2.342406 TCACCTCCAAATCCCTCTCA 57.658 50.000 0.00 0.00 0.00 3.27
1612 1880 4.118410 CAGGAATTCCATCTTCTCTGACG 58.882 47.826 26.22 0.00 38.89 4.35
1721 1989 2.360475 GCCTCCGCTGCTTTCCTT 60.360 61.111 0.00 0.00 0.00 3.36
2004 2272 2.505819 GGTCATAGGAGTCCACCAATGT 59.494 50.000 12.86 0.00 0.00 2.71
2024 2292 4.062293 TGTCGAGTGTTTCCTGTAATTGG 58.938 43.478 0.00 0.00 0.00 3.16
2051 2319 2.998097 CCCCTCCTCGGCATCAAA 59.002 61.111 0.00 0.00 0.00 2.69
2132 2400 4.838423 TCTGTCAAGTCCTCAACAATCCTA 59.162 41.667 0.00 0.00 0.00 2.94
2681 2949 7.921786 TTCATTCAAAGGATCGACATTTAGT 57.078 32.000 0.00 0.00 31.17 2.24
2876 3149 2.548480 AGCTTTGTGTTTCGAACTAGGC 59.452 45.455 0.00 0.00 0.00 3.93
2880 3153 3.006940 TGTGAGCTTTGTGTTTCGAACT 58.993 40.909 0.00 0.00 0.00 3.01
3317 3971 3.778619 GGCAAACAAAACCTTGGCT 57.221 47.368 1.53 0.00 42.95 4.75
3346 4000 9.430623 TCTATTTCATATTCTTGTCAACGTTGA 57.569 29.630 26.53 26.53 34.20 3.18
3455 4109 3.095912 ACCCAAAACCAGCCCTATAAC 57.904 47.619 0.00 0.00 0.00 1.89
3606 4275 9.862371 CTAAATATTGCAGAATCTACTCCGTAT 57.138 33.333 0.00 0.00 0.00 3.06
3628 4297 4.947388 AGAACAGTGAGTTTGCCAACTAAA 59.053 37.500 2.67 0.00 43.79 1.85
3675 4344 9.859427 TCAAAACAATAAAATGCAGAATCCTAG 57.141 29.630 0.00 0.00 0.00 3.02
3747 4416 1.365028 AGGAACAGGGGGAACTAGCTA 59.635 52.381 0.00 0.00 0.00 3.32
3753 4422 1.685820 CAGGAGGAACAGGGGGAAC 59.314 63.158 0.00 0.00 0.00 3.62
3770 4439 2.606519 AAGCGGAGGGTGTAGGCA 60.607 61.111 0.00 0.00 0.00 4.75
3854 5326 7.308782 ACATTGATCTAGTCGACCAAATTTC 57.691 36.000 13.01 3.07 0.00 2.17
3864 5336 3.186909 TGCCGAAACATTGATCTAGTCG 58.813 45.455 0.00 0.00 0.00 4.18
3867 5339 6.554419 TCAAATTGCCGAAACATTGATCTAG 58.446 36.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.