Multiple sequence alignment - TraesCS2A01G301500

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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 TraesCS2A01G301500 chr2A 100.000 2625 0 0 294 2918 516531167 516533791 0.000000e+00 4848.0
1 TraesCS2A01G301500 chr2A 100.000 139 0 0 1 139 516530874 516531012 1.040000e-64 257.0
2 TraesCS2A01G301500 chr2A 87.013 154 17 2 1318 1468 516532146 516532299 1.390000e-38 171.0
3 TraesCS2A01G301500 chr2A 87.013 154 17 2 1273 1426 516532191 516532341 1.390000e-38 171.0
4 TraesCS2A01G301500 chr2A 90.110 91 6 3 2830 2918 593651071 593651160 6.610000e-22 115.0
5 TraesCS2A01G301500 chr2D 91.189 1850 92 30 296 2104 382194881 382196700 0.000000e+00 2447.0
6 TraesCS2A01G301500 chr2D 90.724 442 35 3 2315 2753 382196850 382197288 4.190000e-163 584.0
7 TraesCS2A01G301500 chr2D 94.203 138 6 1 1 136 394637612 394637749 2.950000e-50 209.0
8 TraesCS2A01G301500 chr2D 94.203 138 6 1 1 136 507610734 507610871 2.950000e-50 209.0
9 TraesCS2A01G301500 chr2D 93.617 141 5 2 1 137 539545619 539545759 1.060000e-49 207.0
10 TraesCS2A01G301500 chr2D 89.516 124 10 3 1303 1426 382195944 382196064 1.400000e-33 154.0
11 TraesCS2A01G301500 chr2D 86.154 65 4 4 2830 2892 320359284 320359223 6.750000e-07 65.8
12 TraesCS2A01G301500 chr2B 95.077 711 31 3 761 1468 453077731 453078440 0.000000e+00 1116.0
13 TraesCS2A01G301500 chr2B 91.774 778 36 15 1273 2042 453078287 453079044 0.000000e+00 1057.0
14 TraesCS2A01G301500 chr2B 86.728 324 30 7 2512 2833 453081078 453081390 5.980000e-92 348.0
15 TraesCS2A01G301500 chr2B 90.000 140 14 0 1287 1426 453078343 453078482 6.420000e-42 182.0
16 TraesCS2A01G301500 chr2B 87.421 159 14 4 1318 1471 453078242 453078399 8.310000e-41 178.0
17 TraesCS2A01G301500 chr2B 76.923 143 24 7 2164 2303 140527391 140527255 4.030000e-09 73.1
18 TraesCS2A01G301500 chr2B 89.474 57 4 2 2825 2881 334699178 334699232 1.450000e-08 71.3
19 TraesCS2A01G301500 chr2B 97.222 36 1 0 1433 1468 453078273 453078308 8.730000e-06 62.1
20 TraesCS2A01G301500 chr1D 94.406 143 4 2 1 139 363851436 363851578 1.760000e-52 217.0
21 TraesCS2A01G301500 chr1D 94.245 139 5 2 1 136 161497941 161498079 2.950000e-50 209.0
22 TraesCS2A01G301500 chr1D 93.617 141 7 1 1 139 467993137 467993277 2.950000e-50 209.0
23 TraesCS2A01G301500 chr1D 93.007 143 6 2 1 139 133358805 133358663 3.810000e-49 206.0
24 TraesCS2A01G301500 chr1D 93.007 143 6 2 1 139 188571713 188571571 3.810000e-49 206.0
25 TraesCS2A01G301500 chr5D 94.286 140 4 2 1 136 287090700 287090839 8.190000e-51 211.0
26 TraesCS2A01G301500 chr5D 86.577 149 16 4 2164 2310 525123801 525123947 8.370000e-36 161.0
27 TraesCS2A01G301500 chr5D 85.616 146 21 0 2163 2308 63552404 63552259 1.400000e-33 154.0
28 TraesCS2A01G301500 chr5D 82.500 160 24 1 2151 2310 391992375 391992530 1.410000e-28 137.0
29 TraesCS2A01G301500 chr5D 78.395 162 31 4 2151 2310 15356049 15355890 5.140000e-18 102.0
30 TraesCS2A01G301500 chr5D 82.222 90 15 1 2829 2918 532000527 532000615 3.120000e-10 76.8
31 TraesCS2A01G301500 chr6D 88.079 151 18 0 2160 2310 453001376 453001226 2.310000e-41 180.0
32 TraesCS2A01G301500 chr3D 89.362 141 15 0 2168 2308 550457244 550457104 8.310000e-41 178.0
33 TraesCS2A01G301500 chr3D 93.548 62 4 0 521 582 611168468 611168529 3.100000e-15 93.5
34 TraesCS2A01G301500 chr3D 93.548 62 4 0 521 582 611178103 611178164 3.100000e-15 93.5
35 TraesCS2A01G301500 chr5A 87.075 147 19 0 2164 2310 622123109 622122963 1.800000e-37 167.0
36 TraesCS2A01G301500 chrUn 83.553 152 25 0 2151 2302 467523595 467523746 3.030000e-30 143.0
37 TraesCS2A01G301500 chr7B 87.037 108 12 2 2196 2303 635907104 635907209 1.420000e-23 121.0
38 TraesCS2A01G301500 chr7B 92.593 54 2 2 2829 2881 740483730 740483782 3.120000e-10 76.8
39 TraesCS2A01G301500 chr7B 92.593 54 1 3 2829 2881 439851935 439851986 1.120000e-09 75.0
40 TraesCS2A01G301500 chr6B 89.011 91 6 3 2830 2918 276669952 276669864 3.070000e-20 110.0
41 TraesCS2A01G301500 chr4D 87.500 80 10 0 1511 1590 88700775 88700854 3.100000e-15 93.5
42 TraesCS2A01G301500 chr4B 87.500 80 10 0 1511 1590 125481641 125481720 3.100000e-15 93.5
43 TraesCS2A01G301500 chr4A 85.000 80 12 0 1511 1590 501468716 501468795 6.700000e-12 82.4
44 TraesCS2A01G301500 chr7D 90.566 53 5 0 2829 2881 81808069 81808017 1.450000e-08 71.3
45 TraesCS2A01G301500 chr7A 85.333 75 4 5 2830 2903 547116704 547116772 1.450000e-08 71.3


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 TraesCS2A01G301500 chr2A 516530874 516533791 2917 False 1361.750000 4848 93.506500 1 2918 4 chr2A.!!$F2 2917
1 TraesCS2A01G301500 chr2D 382194881 382197288 2407 False 1061.666667 2447 90.476333 296 2753 3 chr2D.!!$F4 2457
2 TraesCS2A01G301500 chr2B 453077731 453081390 3659 False 490.516667 1116 91.370333 761 2833 6 chr2B.!!$F2 2072

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
128 129 0.105298 ATAGTTCGGGACCCCCTACC 60.105 60.0 4.46 0.0 42.67 3.18 F
848 878 0.169009 GCTTGCCAAACTGATCGTCC 59.831 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1743 0.028902 GCCCGTTAATTCGCACCATC 59.971 55.0 0.00 0.0 0.00 3.51 R
1959 2039 0.316772 CGCGTATACGTGTGCTAGCT 60.317 55.0 26.58 0.0 44.02 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
28 29 5.426689 TCATAGACAATGAAGCAGGAAGT 57.573 39.130 0.00 0.00 41.75 3.01
29 30 6.544928 TCATAGACAATGAAGCAGGAAGTA 57.455 37.500 0.00 0.00 41.75 2.24
30 31 6.577103 TCATAGACAATGAAGCAGGAAGTAG 58.423 40.000 0.00 0.00 41.75 2.57
31 32 4.213564 AGACAATGAAGCAGGAAGTAGG 57.786 45.455 0.00 0.00 0.00 3.18
32 33 3.054802 AGACAATGAAGCAGGAAGTAGGG 60.055 47.826 0.00 0.00 0.00 3.53
33 34 2.644798 ACAATGAAGCAGGAAGTAGGGT 59.355 45.455 0.00 0.00 0.00 4.34
34 35 3.074538 ACAATGAAGCAGGAAGTAGGGTT 59.925 43.478 0.00 0.00 0.00 4.11
35 36 4.082125 CAATGAAGCAGGAAGTAGGGTTT 58.918 43.478 0.00 0.00 0.00 3.27
36 37 3.876309 TGAAGCAGGAAGTAGGGTTTT 57.124 42.857 0.00 0.00 0.00 2.43
37 38 4.986054 TGAAGCAGGAAGTAGGGTTTTA 57.014 40.909 0.00 0.00 0.00 1.52
38 39 4.648651 TGAAGCAGGAAGTAGGGTTTTAC 58.351 43.478 0.00 0.00 0.00 2.01
39 40 3.715638 AGCAGGAAGTAGGGTTTTACC 57.284 47.619 0.00 0.00 37.60 2.85
40 41 3.257578 AGCAGGAAGTAGGGTTTTACCT 58.742 45.455 0.00 0.00 44.75 3.08
41 42 3.263681 AGCAGGAAGTAGGGTTTTACCTC 59.736 47.826 0.00 0.00 42.09 3.85
42 43 3.621709 GCAGGAAGTAGGGTTTTACCTCC 60.622 52.174 0.00 0.00 42.09 4.30
43 44 3.585732 CAGGAAGTAGGGTTTTACCTCCA 59.414 47.826 4.23 0.00 42.09 3.86
44 45 4.227527 CAGGAAGTAGGGTTTTACCTCCAT 59.772 45.833 4.23 0.00 42.09 3.41
45 46 4.856182 AGGAAGTAGGGTTTTACCTCCATT 59.144 41.667 4.23 0.00 42.09 3.16
46 47 6.034003 AGGAAGTAGGGTTTTACCTCCATTA 58.966 40.000 4.23 0.00 42.09 1.90
47 48 6.506413 AGGAAGTAGGGTTTTACCTCCATTAA 59.494 38.462 4.23 0.00 42.09 1.40
48 49 6.827251 GGAAGTAGGGTTTTACCTCCATTAAG 59.173 42.308 0.00 0.00 42.09 1.85
49 50 7.311486 GGAAGTAGGGTTTTACCTCCATTAAGA 60.311 40.741 0.00 0.00 42.09 2.10
50 51 7.196637 AGTAGGGTTTTACCTCCATTAAGAG 57.803 40.000 0.00 0.00 42.09 2.85
57 58 2.528134 CTCCATTAAGAGGGCCCGA 58.472 57.895 18.44 3.54 0.00 5.14
58 59 0.837272 CTCCATTAAGAGGGCCCGAA 59.163 55.000 18.44 10.12 0.00 4.30
59 60 0.544697 TCCATTAAGAGGGCCCGAAC 59.455 55.000 18.44 12.45 0.00 3.95
60 61 0.465642 CCATTAAGAGGGCCCGAACC 60.466 60.000 18.44 7.31 0.00 3.62
61 62 0.546598 CATTAAGAGGGCCCGAACCT 59.453 55.000 18.44 9.75 42.18 3.50
62 63 0.546598 ATTAAGAGGGCCCGAACCTG 59.453 55.000 18.44 0.00 38.79 4.00
63 64 1.559065 TTAAGAGGGCCCGAACCTGG 61.559 60.000 18.44 0.00 38.79 4.45
71 72 3.970205 CCCGAACCTGGGTAAACAT 57.030 52.632 0.00 0.00 44.76 2.71
72 73 2.209690 CCCGAACCTGGGTAAACATT 57.790 50.000 0.00 0.00 44.76 2.71
73 74 3.353370 CCCGAACCTGGGTAAACATTA 57.647 47.619 0.00 0.00 44.76 1.90
74 75 3.893521 CCCGAACCTGGGTAAACATTAT 58.106 45.455 0.00 0.00 44.76 1.28
75 76 3.881089 CCCGAACCTGGGTAAACATTATC 59.119 47.826 0.00 0.00 44.76 1.75
76 77 3.881089 CCGAACCTGGGTAAACATTATCC 59.119 47.826 0.00 0.00 0.00 2.59
77 78 4.384868 CCGAACCTGGGTAAACATTATCCT 60.385 45.833 0.00 0.00 0.00 3.24
78 79 5.190677 CGAACCTGGGTAAACATTATCCTT 58.809 41.667 0.00 0.00 0.00 3.36
79 80 5.650703 CGAACCTGGGTAAACATTATCCTTT 59.349 40.000 0.00 0.00 0.00 3.11
80 81 6.404293 CGAACCTGGGTAAACATTATCCTTTG 60.404 42.308 0.00 0.00 0.00 2.77
81 82 5.899278 ACCTGGGTAAACATTATCCTTTGT 58.101 37.500 0.00 0.00 0.00 2.83
82 83 5.949952 ACCTGGGTAAACATTATCCTTTGTC 59.050 40.000 0.00 0.00 0.00 3.18
83 84 6.187682 CCTGGGTAAACATTATCCTTTGTCT 58.812 40.000 1.45 0.00 0.00 3.41
84 85 6.318900 CCTGGGTAAACATTATCCTTTGTCTC 59.681 42.308 1.45 0.00 0.00 3.36
85 86 6.184789 TGGGTAAACATTATCCTTTGTCTCC 58.815 40.000 1.45 0.00 0.00 3.71
86 87 6.011981 TGGGTAAACATTATCCTTTGTCTCCT 60.012 38.462 1.45 0.00 0.00 3.69
87 88 6.318900 GGGTAAACATTATCCTTTGTCTCCTG 59.681 42.308 0.00 0.00 0.00 3.86
88 89 6.884836 GGTAAACATTATCCTTTGTCTCCTGT 59.115 38.462 0.00 0.00 0.00 4.00
89 90 7.393515 GGTAAACATTATCCTTTGTCTCCTGTT 59.606 37.037 0.00 0.00 0.00 3.16
90 91 9.444600 GTAAACATTATCCTTTGTCTCCTGTTA 57.555 33.333 0.00 0.00 0.00 2.41
91 92 7.923414 AACATTATCCTTTGTCTCCTGTTAC 57.077 36.000 0.00 0.00 0.00 2.50
92 93 6.415573 ACATTATCCTTTGTCTCCTGTTACC 58.584 40.000 0.00 0.00 0.00 2.85
93 94 6.215636 ACATTATCCTTTGTCTCCTGTTACCT 59.784 38.462 0.00 0.00 0.00 3.08
94 95 6.697641 TTATCCTTTGTCTCCTGTTACCTT 57.302 37.500 0.00 0.00 0.00 3.50
95 96 4.618920 TCCTTTGTCTCCTGTTACCTTC 57.381 45.455 0.00 0.00 0.00 3.46
96 97 3.006537 TCCTTTGTCTCCTGTTACCTTCG 59.993 47.826 0.00 0.00 0.00 3.79
97 98 3.006537 CCTTTGTCTCCTGTTACCTTCGA 59.993 47.826 0.00 0.00 0.00 3.71
98 99 4.322801 CCTTTGTCTCCTGTTACCTTCGAT 60.323 45.833 0.00 0.00 0.00 3.59
99 100 4.451629 TTGTCTCCTGTTACCTTCGATC 57.548 45.455 0.00 0.00 0.00 3.69
100 101 2.758979 TGTCTCCTGTTACCTTCGATCC 59.241 50.000 0.00 0.00 0.00 3.36
101 102 3.025262 GTCTCCTGTTACCTTCGATCCT 58.975 50.000 0.00 0.00 0.00 3.24
102 103 3.067040 GTCTCCTGTTACCTTCGATCCTC 59.933 52.174 0.00 0.00 0.00 3.71
103 104 3.024547 CTCCTGTTACCTTCGATCCTCA 58.975 50.000 0.00 0.00 0.00 3.86
104 105 3.024547 TCCTGTTACCTTCGATCCTCAG 58.975 50.000 0.00 0.00 0.00 3.35
105 106 3.024547 CCTGTTACCTTCGATCCTCAGA 58.975 50.000 0.00 0.00 0.00 3.27
106 107 3.181485 CCTGTTACCTTCGATCCTCAGAC 60.181 52.174 0.00 0.00 0.00 3.51
107 108 2.422479 TGTTACCTTCGATCCTCAGACG 59.578 50.000 0.00 0.00 0.00 4.18
108 109 1.022735 TACCTTCGATCCTCAGACGC 58.977 55.000 0.00 0.00 0.00 5.19
109 110 0.965866 ACCTTCGATCCTCAGACGCA 60.966 55.000 0.00 0.00 0.00 5.24
110 111 0.387202 CCTTCGATCCTCAGACGCAT 59.613 55.000 0.00 0.00 0.00 4.73
111 112 1.609072 CCTTCGATCCTCAGACGCATA 59.391 52.381 0.00 0.00 0.00 3.14
112 113 2.351253 CCTTCGATCCTCAGACGCATAG 60.351 54.545 0.00 0.00 0.00 2.23
113 114 1.968704 TCGATCCTCAGACGCATAGT 58.031 50.000 0.00 0.00 0.00 2.12
114 115 2.298610 TCGATCCTCAGACGCATAGTT 58.701 47.619 0.00 0.00 0.00 2.24
115 116 2.290916 TCGATCCTCAGACGCATAGTTC 59.709 50.000 0.00 0.00 0.00 3.01
116 117 2.656085 GATCCTCAGACGCATAGTTCG 58.344 52.381 0.00 0.00 0.00 3.95
117 118 0.738975 TCCTCAGACGCATAGTTCGG 59.261 55.000 0.00 0.00 0.00 4.30
118 119 0.249073 CCTCAGACGCATAGTTCGGG 60.249 60.000 0.00 0.00 0.00 5.14
119 120 0.738975 CTCAGACGCATAGTTCGGGA 59.261 55.000 0.00 0.00 0.00 5.14
120 121 0.454600 TCAGACGCATAGTTCGGGAC 59.545 55.000 0.00 0.00 0.00 4.46
121 122 0.527817 CAGACGCATAGTTCGGGACC 60.528 60.000 0.00 0.00 0.00 4.46
122 123 1.227176 GACGCATAGTTCGGGACCC 60.227 63.158 0.00 0.00 0.00 4.46
123 124 2.108362 CGCATAGTTCGGGACCCC 59.892 66.667 4.46 0.00 0.00 4.95
124 125 2.509422 GCATAGTTCGGGACCCCC 59.491 66.667 4.46 0.00 41.09 5.40
125 126 2.070650 GCATAGTTCGGGACCCCCT 61.071 63.158 4.46 0.84 42.67 4.79
126 127 0.761702 GCATAGTTCGGGACCCCCTA 60.762 60.000 4.46 3.30 42.67 3.53
127 128 1.046204 CATAGTTCGGGACCCCCTAC 58.954 60.000 4.46 0.29 42.67 3.18
128 129 0.105298 ATAGTTCGGGACCCCCTACC 60.105 60.000 4.46 0.00 42.67 3.18
129 130 2.242408 TAGTTCGGGACCCCCTACCC 62.242 65.000 4.46 0.00 42.67 3.69
133 134 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
134 135 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
135 136 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
136 137 1.232216 GACCCCCTACCCGAGATCA 59.768 63.158 0.00 0.00 0.00 2.92
137 138 0.828343 GACCCCCTACCCGAGATCAG 60.828 65.000 0.00 0.00 0.00 2.90
138 139 2.210711 CCCCCTACCCGAGATCAGC 61.211 68.421 0.00 0.00 0.00 4.26
355 356 3.359002 CTTGTTGAGCTGGTGCCC 58.641 61.111 0.00 0.00 40.80 5.36
359 360 1.228245 GTTGAGCTGGTGCCCTCAA 60.228 57.895 0.00 6.02 43.60 3.02
360 361 0.610232 GTTGAGCTGGTGCCCTCAAT 60.610 55.000 11.27 0.00 46.24 2.57
365 366 1.065126 AGCTGGTGCCCTCAATAGAAC 60.065 52.381 0.00 0.00 40.80 3.01
374 375 6.405842 GGTGCCCTCAATAGAACCTTTATTTG 60.406 42.308 0.00 0.00 0.00 2.32
400 401 7.065443 GTGTACTTCTTGTTTGTACTTTGGTCT 59.935 37.037 0.00 0.00 37.85 3.85
401 402 6.679327 ACTTCTTGTTTGTACTTTGGTCTC 57.321 37.500 0.00 0.00 0.00 3.36
403 404 4.761975 TCTTGTTTGTACTTTGGTCTCGT 58.238 39.130 0.00 0.00 0.00 4.18
421 450 1.668751 CGTGTGTGTTGCTACCTTGTT 59.331 47.619 0.00 0.00 0.00 2.83
442 471 2.372264 AGGCTTGATGTATGCTTGTGG 58.628 47.619 0.00 0.00 0.00 4.17
443 472 1.202336 GGCTTGATGTATGCTTGTGGC 60.202 52.381 0.00 0.00 42.22 5.01
444 473 1.532505 GCTTGATGTATGCTTGTGGCG 60.533 52.381 0.00 0.00 45.43 5.69
450 479 0.732538 GTATGCTTGTGGCGGTTTGC 60.733 55.000 0.00 0.00 45.43 3.68
455 484 1.336795 GCTTGTGGCGGTTTGCTTTAT 60.337 47.619 0.00 0.00 45.43 1.40
456 485 2.094957 GCTTGTGGCGGTTTGCTTTATA 60.095 45.455 0.00 0.00 45.43 0.98
457 486 3.498082 CTTGTGGCGGTTTGCTTTATAC 58.502 45.455 0.00 0.00 45.43 1.47
499 529 7.907214 AAGCCATTTCGGTATATGAGATTAC 57.093 36.000 0.00 0.00 36.97 1.89
500 530 7.004555 AGCCATTTCGGTATATGAGATTACA 57.995 36.000 0.00 0.00 36.97 2.41
543 573 3.756434 GAGTATTTGGCCTAAAGTGTGCA 59.244 43.478 3.32 0.00 0.00 4.57
546 576 3.658757 TTTGGCCTAAAGTGTGCAATC 57.341 42.857 3.32 0.00 0.00 2.67
548 578 1.885887 TGGCCTAAAGTGTGCAATCAC 59.114 47.619 3.32 0.00 43.40 3.06
559 589 6.152932 AGTGTGCAATCACTTTGAATTTCT 57.847 33.333 4.21 0.00 44.92 2.52
561 591 5.176223 GTGTGCAATCACTTTGAATTTCTGG 59.824 40.000 0.38 0.00 43.49 3.86
562 592 5.068855 TGTGCAATCACTTTGAATTTCTGGA 59.931 36.000 0.00 0.00 43.49 3.86
563 593 5.403466 GTGCAATCACTTTGAATTTCTGGAC 59.597 40.000 0.00 0.00 40.03 4.02
587 617 8.539770 ACTAATGACACATTTCACTCTACAAG 57.460 34.615 2.40 0.00 0.00 3.16
588 618 5.869753 ATGACACATTTCACTCTACAAGC 57.130 39.130 0.00 0.00 0.00 4.01
589 619 4.960938 TGACACATTTCACTCTACAAGCT 58.039 39.130 0.00 0.00 0.00 3.74
591 621 4.960938 ACACATTTCACTCTACAAGCTCA 58.039 39.130 0.00 0.00 0.00 4.26
592 622 5.555017 ACACATTTCACTCTACAAGCTCAT 58.445 37.500 0.00 0.00 0.00 2.90
609 639 5.585390 AGCTCATGAGTTTCAACAAGTTTG 58.415 37.500 23.38 0.00 0.00 2.93
615 645 1.852280 GTTTCAACAAGTTTGCTCCGC 59.148 47.619 0.00 0.00 0.00 5.54
617 647 0.944386 TCAACAAGTTTGCTCCGCTC 59.056 50.000 0.00 0.00 0.00 5.03
621 651 0.514691 CAAGTTTGCTCCGCTCAGAC 59.485 55.000 0.00 0.00 0.00 3.51
628 658 1.137825 CTCCGCTCAGACGAAGGTC 59.862 63.158 0.00 0.00 43.76 3.85
650 680 0.460284 AGGCGACTTGCTTACGGATG 60.460 55.000 0.00 0.00 45.43 3.51
652 682 1.631072 CGACTTGCTTACGGATGCG 59.369 57.895 4.58 4.58 0.00 4.73
653 683 1.076533 CGACTTGCTTACGGATGCGT 61.077 55.000 18.47 18.47 0.00 5.24
679 709 1.852633 TGGATGCTCGAGGAAGAAGA 58.147 50.000 11.77 0.00 0.00 2.87
680 710 1.478510 TGGATGCTCGAGGAAGAAGAC 59.521 52.381 11.77 0.00 0.00 3.01
686 716 2.289133 GCTCGAGGAAGAAGACTTTGGT 60.289 50.000 15.58 0.00 36.39 3.67
697 727 6.464530 AGAAGACTTTGGTACCCCTAAAAT 57.535 37.500 10.07 0.00 0.00 1.82
744 774 8.894768 TGGATGTTTTTATAAGGGTTTGTTTG 57.105 30.769 0.00 0.00 0.00 2.93
764 794 9.823647 TTGTTTGCTTAAATATGACCAAAAAGA 57.176 25.926 0.00 0.00 0.00 2.52
843 873 1.741706 CGATCTGCTTGCCAAACTGAT 59.258 47.619 0.51 0.51 0.00 2.90
848 878 0.169009 GCTTGCCAAACTGATCGTCC 59.831 55.000 0.00 0.00 0.00 4.79
1084 1114 2.167398 GACCAGCAACGAGGGCTACA 62.167 60.000 0.00 0.00 40.23 2.74
1251 1281 0.511221 CCGGTTACAACAAGCAGTCG 59.489 55.000 0.00 0.00 0.00 4.18
1332 1362 1.588082 GTACAAGAAGTCCGGCGGA 59.412 57.895 27.46 27.46 0.00 5.54
1418 1493 0.672711 GGGTACAAGAAGTCGGGTGC 60.673 60.000 0.00 0.00 0.00 5.01
1610 1688 2.904697 ACCTCCCGAACGATATTTCC 57.095 50.000 0.00 0.00 0.00 3.13
1620 1698 1.593006 ACGATATTTCCTCGCGCAAAG 59.407 47.619 8.75 3.65 39.71 2.77
1630 1708 1.398390 CTCGCGCAAAGATTTTAGGCT 59.602 47.619 8.75 0.00 0.00 4.58
1662 1740 2.935849 CGTTTCCACCGATGATGATTCA 59.064 45.455 0.00 0.00 36.00 2.57
1663 1741 3.373748 CGTTTCCACCGATGATGATTCAA 59.626 43.478 0.00 0.00 34.96 2.69
1664 1742 4.035558 CGTTTCCACCGATGATGATTCAAT 59.964 41.667 0.00 0.00 34.96 2.57
1665 1743 5.276270 GTTTCCACCGATGATGATTCAATG 58.724 41.667 0.00 0.00 34.96 2.82
1872 1952 3.437795 GACGGCGAGGACGAGGAA 61.438 66.667 16.62 0.00 42.66 3.36
1959 2039 1.200252 GATCCGCGATTCAGCTAGCTA 59.800 52.381 18.86 2.62 34.40 3.32
1960 2040 0.593618 TCCGCGATTCAGCTAGCTAG 59.406 55.000 18.86 16.84 34.40 3.42
2068 2412 2.323105 GTCGGTGTGCGTGTGTTG 59.677 61.111 0.00 0.00 0.00 3.33
2069 2413 3.568743 TCGGTGTGCGTGTGTTGC 61.569 61.111 0.00 0.00 0.00 4.17
2073 2417 0.457681 GGTGTGCGTGTGTTGCTTTT 60.458 50.000 0.00 0.00 0.00 2.27
2074 2418 1.345410 GTGTGCGTGTGTTGCTTTTT 58.655 45.000 0.00 0.00 0.00 1.94
2104 2448 2.405805 TGTGCGTGTGTTGCTGCTT 61.406 52.632 0.00 0.00 0.00 3.91
2105 2449 1.092345 TGTGCGTGTGTTGCTGCTTA 61.092 50.000 0.00 0.00 0.00 3.09
2106 2450 0.657368 GTGCGTGTGTTGCTGCTTAC 60.657 55.000 0.00 0.00 0.00 2.34
2107 2451 1.092345 TGCGTGTGTTGCTGCTTACA 61.092 50.000 0.00 2.54 0.00 2.41
2108 2452 0.028770 GCGTGTGTTGCTGCTTACAA 59.971 50.000 9.18 0.00 0.00 2.41
2120 2565 1.937223 TGCTTACAACGTTGTGTGGAG 59.063 47.619 37.43 28.09 42.31 3.86
2148 2593 2.804697 TAACTTGCTGCGTGTCTACA 57.195 45.000 0.00 0.00 0.00 2.74
2152 2597 3.190079 ACTTGCTGCGTGTCTACATATG 58.810 45.455 0.00 0.00 0.00 1.78
2153 2598 2.959507 TGCTGCGTGTCTACATATGT 57.040 45.000 13.93 13.93 0.00 2.29
2154 2599 4.142249 ACTTGCTGCGTGTCTACATATGTA 60.142 41.667 14.75 14.75 0.00 2.29
2155 2600 3.702330 TGCTGCGTGTCTACATATGTAC 58.298 45.455 11.62 6.64 0.00 2.90
2156 2601 3.380320 TGCTGCGTGTCTACATATGTACT 59.620 43.478 11.62 0.00 0.00 2.73
2157 2602 4.142249 TGCTGCGTGTCTACATATGTACTT 60.142 41.667 11.62 0.00 0.00 2.24
2158 2603 4.207224 GCTGCGTGTCTACATATGTACTTG 59.793 45.833 11.62 3.09 0.00 3.16
2159 2604 4.109766 TGCGTGTCTACATATGTACTTGC 58.890 43.478 11.62 13.12 0.00 4.01
2160 2605 4.142249 TGCGTGTCTACATATGTACTTGCT 60.142 41.667 11.62 0.00 0.00 3.91
2161 2606 4.441415 GCGTGTCTACATATGTACTTGCTC 59.559 45.833 11.62 3.32 0.00 4.26
2162 2607 5.733655 GCGTGTCTACATATGTACTTGCTCT 60.734 44.000 11.62 0.00 0.00 4.09
2163 2608 5.683302 CGTGTCTACATATGTACTTGCTCTG 59.317 44.000 11.62 0.27 0.00 3.35
2164 2609 6.565234 GTGTCTACATATGTACTTGCTCTGT 58.435 40.000 11.62 0.00 0.00 3.41
2165 2610 7.036220 GTGTCTACATATGTACTTGCTCTGTT 58.964 38.462 11.62 0.00 0.00 3.16
2166 2611 7.545965 GTGTCTACATATGTACTTGCTCTGTTT 59.454 37.037 11.62 0.00 0.00 2.83
2167 2612 7.759886 TGTCTACATATGTACTTGCTCTGTTTC 59.240 37.037 11.62 0.00 0.00 2.78
2168 2613 7.976734 GTCTACATATGTACTTGCTCTGTTTCT 59.023 37.037 11.62 0.00 0.00 2.52
2169 2614 9.185680 TCTACATATGTACTTGCTCTGTTTCTA 57.814 33.333 11.62 0.00 0.00 2.10
2170 2615 9.803315 CTACATATGTACTTGCTCTGTTTCTAA 57.197 33.333 11.62 0.00 0.00 2.10
2172 2617 9.672673 ACATATGTACTTGCTCTGTTTCTAAAT 57.327 29.630 6.56 0.00 0.00 1.40
2180 2625 9.289782 ACTTGCTCTGTTTCTAAATATTTGTCT 57.710 29.630 11.05 0.00 0.00 3.41
2181 2626 9.766277 CTTGCTCTGTTTCTAAATATTTGTCTC 57.234 33.333 11.05 0.00 0.00 3.36
2182 2627 9.507329 TTGCTCTGTTTCTAAATATTTGTCTCT 57.493 29.630 11.05 0.00 0.00 3.10
2215 2660 6.998258 TTAACAAGTGACTACTTACGAAGC 57.002 37.500 0.00 0.00 45.12 3.86
2216 2661 4.579454 ACAAGTGACTACTTACGAAGCA 57.421 40.909 0.00 0.00 45.12 3.91
2217 2662 4.940463 ACAAGTGACTACTTACGAAGCAA 58.060 39.130 0.00 0.00 45.12 3.91
2218 2663 5.353938 ACAAGTGACTACTTACGAAGCAAA 58.646 37.500 0.00 0.00 45.12 3.68
2219 2664 5.813672 ACAAGTGACTACTTACGAAGCAAAA 59.186 36.000 0.00 0.00 45.12 2.44
2220 2665 6.482308 ACAAGTGACTACTTACGAAGCAAAAT 59.518 34.615 0.00 0.00 45.12 1.82
2221 2666 6.467723 AGTGACTACTTACGAAGCAAAATG 57.532 37.500 0.00 0.00 31.66 2.32
2222 2667 6.220930 AGTGACTACTTACGAAGCAAAATGA 58.779 36.000 0.00 0.00 31.66 2.57
2223 2668 6.366332 AGTGACTACTTACGAAGCAAAATGAG 59.634 38.462 0.00 0.00 31.66 2.90
2224 2669 6.365247 GTGACTACTTACGAAGCAAAATGAGA 59.635 38.462 0.00 0.00 0.00 3.27
2225 2670 6.926826 TGACTACTTACGAAGCAAAATGAGAA 59.073 34.615 0.00 0.00 0.00 2.87
2226 2671 7.439955 TGACTACTTACGAAGCAAAATGAGAAA 59.560 33.333 0.00 0.00 0.00 2.52
2227 2672 8.149973 ACTACTTACGAAGCAAAATGAGAAAA 57.850 30.769 0.00 0.00 0.00 2.29
2228 2673 8.784043 ACTACTTACGAAGCAAAATGAGAAAAT 58.216 29.630 0.00 0.00 0.00 1.82
2229 2674 9.267096 CTACTTACGAAGCAAAATGAGAAAATC 57.733 33.333 0.00 0.00 0.00 2.17
2230 2675 7.875971 ACTTACGAAGCAAAATGAGAAAATCT 58.124 30.769 0.00 0.00 0.00 2.40
2231 2676 8.999431 ACTTACGAAGCAAAATGAGAAAATCTA 58.001 29.630 0.00 0.00 0.00 1.98
2232 2677 9.267096 CTTACGAAGCAAAATGAGAAAATCTAC 57.733 33.333 0.00 0.00 0.00 2.59
2233 2678 7.202016 ACGAAGCAAAATGAGAAAATCTACA 57.798 32.000 0.00 0.00 0.00 2.74
2234 2679 7.078228 ACGAAGCAAAATGAGAAAATCTACAC 58.922 34.615 0.00 0.00 0.00 2.90
2235 2680 7.041098 ACGAAGCAAAATGAGAAAATCTACACT 60.041 33.333 0.00 0.00 0.00 3.55
2236 2681 7.805071 CGAAGCAAAATGAGAAAATCTACACTT 59.195 33.333 0.00 0.00 0.00 3.16
2237 2682 9.468532 GAAGCAAAATGAGAAAATCTACACTTT 57.531 29.630 0.00 0.00 0.00 2.66
2343 2789 5.833406 TGTATGTATTGTTTCTGCATGGG 57.167 39.130 0.00 0.00 0.00 4.00
2373 2820 9.442047 AGTATCGAGAATTCAATCAGTTCTTTT 57.558 29.630 8.44 0.00 32.67 2.27
2490 4365 7.895429 AGAGGATTGGAATTTCTCATGGTTTTA 59.105 33.333 0.00 0.00 0.00 1.52
2620 4527 6.029346 TGGAAAGAGGATTCTCATTTTTGC 57.971 37.500 3.21 1.49 42.34 3.68
2697 4606 7.610305 TGGAGATGGTAAAAATAACAGGTTCTC 59.390 37.037 0.00 0.00 0.00 2.87
2709 4618 7.893124 ATAACAGGTTCTCGGAAGATTAGTA 57.107 36.000 0.00 0.00 40.84 1.82
2720 4629 4.024218 CGGAAGATTAGTAGGTAGGTGACG 60.024 50.000 0.00 0.00 0.00 4.35
2749 4658 7.775561 CCTTTGAAAGTGGCTTATCCTATACTT 59.224 37.037 4.02 0.00 31.96 2.24
2803 4712 4.022935 TGTGGTTGATGTCATTGAGAAAGC 60.023 41.667 0.00 0.00 0.00 3.51
2824 4733 9.785982 GAAAGCTAGGGATAATTTTACTCTCAT 57.214 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.324770 TCCTGCTTCATTGTCTATGATGAGTA 59.675 38.462 12.31 1.98 42.69 2.59
2 3 5.608449 TCCTGCTTCATTGTCTATGATGAG 58.392 41.667 12.31 3.81 42.69 2.90
3 4 5.619132 TCCTGCTTCATTGTCTATGATGA 57.381 39.130 12.31 0.00 42.69 2.92
4 5 5.821470 ACTTCCTGCTTCATTGTCTATGATG 59.179 40.000 0.00 2.41 42.69 3.07
5 6 5.999044 ACTTCCTGCTTCATTGTCTATGAT 58.001 37.500 0.00 0.00 42.69 2.45
6 7 5.426689 ACTTCCTGCTTCATTGTCTATGA 57.573 39.130 0.00 0.00 41.50 2.15
7 8 5.757320 CCTACTTCCTGCTTCATTGTCTATG 59.243 44.000 0.00 0.00 35.45 2.23
8 9 5.163258 CCCTACTTCCTGCTTCATTGTCTAT 60.163 44.000 0.00 0.00 0.00 1.98
9 10 4.162320 CCCTACTTCCTGCTTCATTGTCTA 59.838 45.833 0.00 0.00 0.00 2.59
10 11 3.054802 CCCTACTTCCTGCTTCATTGTCT 60.055 47.826 0.00 0.00 0.00 3.41
11 12 3.274288 CCCTACTTCCTGCTTCATTGTC 58.726 50.000 0.00 0.00 0.00 3.18
12 13 2.644798 ACCCTACTTCCTGCTTCATTGT 59.355 45.455 0.00 0.00 0.00 2.71
13 14 3.356529 ACCCTACTTCCTGCTTCATTG 57.643 47.619 0.00 0.00 0.00 2.82
14 15 4.388577 AAACCCTACTTCCTGCTTCATT 57.611 40.909 0.00 0.00 0.00 2.57
15 16 4.388577 AAAACCCTACTTCCTGCTTCAT 57.611 40.909 0.00 0.00 0.00 2.57
16 17 3.876309 AAAACCCTACTTCCTGCTTCA 57.124 42.857 0.00 0.00 0.00 3.02
17 18 4.008330 GGTAAAACCCTACTTCCTGCTTC 58.992 47.826 0.00 0.00 30.04 3.86
18 19 3.656264 AGGTAAAACCCTACTTCCTGCTT 59.344 43.478 0.00 0.00 39.75 3.91
19 20 3.257578 AGGTAAAACCCTACTTCCTGCT 58.742 45.455 0.00 0.00 39.75 4.24
20 21 3.607741 GAGGTAAAACCCTACTTCCTGC 58.392 50.000 0.00 0.00 39.75 4.85
21 22 3.585732 TGGAGGTAAAACCCTACTTCCTG 59.414 47.826 11.71 0.00 44.50 3.86
22 23 3.878086 TGGAGGTAAAACCCTACTTCCT 58.122 45.455 11.71 0.00 44.50 3.36
23 24 4.857130 ATGGAGGTAAAACCCTACTTCC 57.143 45.455 5.26 5.26 44.47 3.46
24 25 7.627311 TCTTAATGGAGGTAAAACCCTACTTC 58.373 38.462 0.00 0.00 39.75 3.01
25 26 7.311739 CCTCTTAATGGAGGTAAAACCCTACTT 60.312 40.741 3.13 0.00 45.65 2.24
26 27 6.158169 CCTCTTAATGGAGGTAAAACCCTACT 59.842 42.308 3.13 0.00 45.65 2.57
27 28 6.354938 CCTCTTAATGGAGGTAAAACCCTAC 58.645 44.000 3.13 0.00 45.65 3.18
28 29 6.570654 CCTCTTAATGGAGGTAAAACCCTA 57.429 41.667 3.13 0.00 45.65 3.53
29 30 5.452341 CCTCTTAATGGAGGTAAAACCCT 57.548 43.478 3.13 0.00 45.65 4.34
39 40 0.837272 TTCGGGCCCTCTTAATGGAG 59.163 55.000 22.43 0.00 0.00 3.86
40 41 0.544697 GTTCGGGCCCTCTTAATGGA 59.455 55.000 22.43 3.53 0.00 3.41
41 42 0.465642 GGTTCGGGCCCTCTTAATGG 60.466 60.000 22.43 0.54 0.00 3.16
42 43 0.546598 AGGTTCGGGCCCTCTTAATG 59.453 55.000 22.43 1.43 0.00 1.90
43 44 0.546598 CAGGTTCGGGCCCTCTTAAT 59.453 55.000 22.43 0.00 0.00 1.40
44 45 1.559065 CCAGGTTCGGGCCCTCTTAA 61.559 60.000 22.43 5.89 0.00 1.85
45 46 1.993391 CCAGGTTCGGGCCCTCTTA 60.993 63.158 22.43 0.00 0.00 2.10
46 47 3.330720 CCAGGTTCGGGCCCTCTT 61.331 66.667 22.43 3.59 0.00 2.85
54 55 3.881089 GGATAATGTTTACCCAGGTTCGG 59.119 47.826 0.00 0.00 0.00 4.30
55 56 4.777463 AGGATAATGTTTACCCAGGTTCG 58.223 43.478 0.00 0.00 0.00 3.95
56 57 6.436218 ACAAAGGATAATGTTTACCCAGGTTC 59.564 38.462 0.00 0.00 0.00 3.62
57 58 6.319715 ACAAAGGATAATGTTTACCCAGGTT 58.680 36.000 0.00 0.00 0.00 3.50
58 59 5.899278 ACAAAGGATAATGTTTACCCAGGT 58.101 37.500 0.00 0.00 0.00 4.00
59 60 6.187682 AGACAAAGGATAATGTTTACCCAGG 58.812 40.000 0.00 0.00 0.00 4.45
60 61 6.318900 GGAGACAAAGGATAATGTTTACCCAG 59.681 42.308 0.00 0.00 0.00 4.45
61 62 6.011981 AGGAGACAAAGGATAATGTTTACCCA 60.012 38.462 0.00 0.00 0.00 4.51
62 63 6.318900 CAGGAGACAAAGGATAATGTTTACCC 59.681 42.308 0.00 0.00 0.00 3.69
63 64 6.884836 ACAGGAGACAAAGGATAATGTTTACC 59.115 38.462 0.00 0.00 0.00 2.85
64 65 7.923414 ACAGGAGACAAAGGATAATGTTTAC 57.077 36.000 0.00 0.00 0.00 2.01
65 66 9.444600 GTAACAGGAGACAAAGGATAATGTTTA 57.555 33.333 0.00 0.00 31.42 2.01
66 67 7.393515 GGTAACAGGAGACAAAGGATAATGTTT 59.606 37.037 0.00 0.00 31.42 2.83
67 68 6.884836 GGTAACAGGAGACAAAGGATAATGTT 59.115 38.462 0.00 0.00 33.36 2.71
68 69 6.215636 AGGTAACAGGAGACAAAGGATAATGT 59.784 38.462 0.00 0.00 41.41 2.71
69 70 6.653989 AGGTAACAGGAGACAAAGGATAATG 58.346 40.000 0.00 0.00 41.41 1.90
70 71 6.893020 AGGTAACAGGAGACAAAGGATAAT 57.107 37.500 0.00 0.00 41.41 1.28
71 72 6.573680 CGAAGGTAACAGGAGACAAAGGATAA 60.574 42.308 0.00 0.00 41.41 1.75
72 73 5.105473 CGAAGGTAACAGGAGACAAAGGATA 60.105 44.000 0.00 0.00 41.41 2.59
73 74 4.322801 CGAAGGTAACAGGAGACAAAGGAT 60.323 45.833 0.00 0.00 41.41 3.24
74 75 3.006537 CGAAGGTAACAGGAGACAAAGGA 59.993 47.826 0.00 0.00 41.41 3.36
75 76 3.006537 TCGAAGGTAACAGGAGACAAAGG 59.993 47.826 0.00 0.00 41.41 3.11
76 77 4.252971 TCGAAGGTAACAGGAGACAAAG 57.747 45.455 0.00 0.00 41.41 2.77
77 78 4.322499 GGATCGAAGGTAACAGGAGACAAA 60.322 45.833 0.00 0.00 41.41 2.83
78 79 3.194968 GGATCGAAGGTAACAGGAGACAA 59.805 47.826 0.00 0.00 41.41 3.18
79 80 2.758979 GGATCGAAGGTAACAGGAGACA 59.241 50.000 0.00 0.00 41.41 3.41
80 81 3.025262 AGGATCGAAGGTAACAGGAGAC 58.975 50.000 0.00 0.00 41.41 3.36
81 82 3.288964 GAGGATCGAAGGTAACAGGAGA 58.711 50.000 0.00 0.00 41.41 3.71
82 83 3.024547 TGAGGATCGAAGGTAACAGGAG 58.975 50.000 0.00 0.00 38.61 3.69
83 84 3.024547 CTGAGGATCGAAGGTAACAGGA 58.975 50.000 0.00 0.00 38.61 3.86
84 85 3.024547 TCTGAGGATCGAAGGTAACAGG 58.975 50.000 0.00 0.00 38.61 4.00
85 86 3.487711 CGTCTGAGGATCGAAGGTAACAG 60.488 52.174 0.00 0.00 38.61 3.16
86 87 2.422479 CGTCTGAGGATCGAAGGTAACA 59.578 50.000 0.00 0.00 38.61 2.41
87 88 2.795331 GCGTCTGAGGATCGAAGGTAAC 60.795 54.545 0.82 0.00 38.61 2.50
88 89 1.404391 GCGTCTGAGGATCGAAGGTAA 59.596 52.381 0.82 0.00 38.61 2.85
89 90 1.022735 GCGTCTGAGGATCGAAGGTA 58.977 55.000 0.82 0.00 38.61 3.08
90 91 0.965866 TGCGTCTGAGGATCGAAGGT 60.966 55.000 0.82 0.00 38.61 3.50
91 92 0.387202 ATGCGTCTGAGGATCGAAGG 59.613 55.000 0.82 0.00 38.61 3.46
92 93 2.292016 ACTATGCGTCTGAGGATCGAAG 59.708 50.000 0.82 0.00 38.61 3.79
93 94 2.298610 ACTATGCGTCTGAGGATCGAA 58.701 47.619 0.82 0.00 38.61 3.71
94 95 1.968704 ACTATGCGTCTGAGGATCGA 58.031 50.000 0.82 0.00 38.61 3.59
95 96 2.656085 GAACTATGCGTCTGAGGATCG 58.344 52.381 0.82 0.00 38.61 3.69
96 97 2.605823 CCGAACTATGCGTCTGAGGATC 60.606 54.545 0.82 0.00 0.00 3.36
97 98 1.338337 CCGAACTATGCGTCTGAGGAT 59.662 52.381 0.82 0.00 0.00 3.24
98 99 0.738975 CCGAACTATGCGTCTGAGGA 59.261 55.000 0.82 0.00 0.00 3.71
99 100 0.249073 CCCGAACTATGCGTCTGAGG 60.249 60.000 0.00 0.00 0.00 3.86
100 101 0.738975 TCCCGAACTATGCGTCTGAG 59.261 55.000 0.00 0.00 0.00 3.35
101 102 0.454600 GTCCCGAACTATGCGTCTGA 59.545 55.000 0.00 0.00 0.00 3.27
102 103 0.527817 GGTCCCGAACTATGCGTCTG 60.528 60.000 0.00 0.00 0.00 3.51
103 104 1.673808 GGGTCCCGAACTATGCGTCT 61.674 60.000 0.00 0.00 0.00 4.18
104 105 1.227176 GGGTCCCGAACTATGCGTC 60.227 63.158 0.00 0.00 0.00 5.19
105 106 2.728435 GGGGTCCCGAACTATGCGT 61.728 63.158 0.48 0.00 0.00 5.24
106 107 2.108362 GGGGTCCCGAACTATGCG 59.892 66.667 0.48 0.00 0.00 4.73
107 108 2.509422 GGGGGTCCCGAACTATGC 59.491 66.667 0.48 0.00 36.85 3.14
116 117 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
117 118 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
118 119 0.828343 CTGATCTCGGGTAGGGGGTC 60.828 65.000 0.00 0.00 0.00 4.46
119 120 1.233369 CTGATCTCGGGTAGGGGGT 59.767 63.158 0.00 0.00 0.00 4.95
120 121 2.210711 GCTGATCTCGGGTAGGGGG 61.211 68.421 0.00 0.00 0.00 5.40
121 122 3.460995 GCTGATCTCGGGTAGGGG 58.539 66.667 0.00 0.00 0.00 4.79
293 294 2.302230 GCACATGCCACACAAACGC 61.302 57.895 0.00 0.00 34.31 4.84
294 295 3.920738 GCACATGCCACACAAACG 58.079 55.556 0.00 0.00 34.31 3.60
360 361 9.841295 ACAAGAAGTACACAAATAAAGGTTCTA 57.159 29.630 0.00 0.00 0.00 2.10
374 375 7.065443 AGACCAAAGTACAAACAAGAAGTACAC 59.935 37.037 0.00 0.00 40.32 2.90
383 384 4.093703 CACACGAGACCAAAGTACAAACAA 59.906 41.667 0.00 0.00 0.00 2.83
395 396 0.747852 TAGCAACACACACGAGACCA 59.252 50.000 0.00 0.00 0.00 4.02
400 401 1.134640 ACAAGGTAGCAACACACACGA 60.135 47.619 0.00 0.00 0.00 4.35
401 402 1.295792 ACAAGGTAGCAACACACACG 58.704 50.000 0.00 0.00 0.00 4.49
403 404 3.472652 CCTAACAAGGTAGCAACACACA 58.527 45.455 0.00 0.00 0.00 3.72
421 450 3.544684 CCACAAGCATACATCAAGCCTA 58.455 45.455 0.00 0.00 0.00 3.93
424 453 1.532505 CGCCACAAGCATACATCAAGC 60.533 52.381 0.00 0.00 44.04 4.01
455 484 6.041182 TGGCTTTCGTCCTGCTTTATATAGTA 59.959 38.462 0.00 0.00 0.00 1.82
456 485 5.163343 TGGCTTTCGTCCTGCTTTATATAGT 60.163 40.000 0.00 0.00 0.00 2.12
457 486 5.297547 TGGCTTTCGTCCTGCTTTATATAG 58.702 41.667 0.00 0.00 0.00 1.31
499 529 8.475331 ACTCGTAAACTGGTCAATTTAGTATG 57.525 34.615 0.00 0.00 0.00 2.39
512 542 3.606687 AGGCCAAATACTCGTAAACTGG 58.393 45.455 5.01 0.00 0.00 4.00
515 545 6.148315 ACACTTTAGGCCAAATACTCGTAAAC 59.852 38.462 5.01 0.00 0.00 2.01
518 548 5.172934 CACACTTTAGGCCAAATACTCGTA 58.827 41.667 5.01 0.00 0.00 3.43
543 573 9.300681 TCATTAGTCCAGAAATTCAAAGTGATT 57.699 29.630 0.00 0.00 0.00 2.57
546 576 7.805071 GTGTCATTAGTCCAGAAATTCAAAGTG 59.195 37.037 0.00 0.00 0.00 3.16
548 578 7.874940 TGTGTCATTAGTCCAGAAATTCAAAG 58.125 34.615 0.00 0.00 0.00 2.77
549 579 7.815840 TGTGTCATTAGTCCAGAAATTCAAA 57.184 32.000 0.00 0.00 0.00 2.69
550 580 8.408043 AATGTGTCATTAGTCCAGAAATTCAA 57.592 30.769 0.00 0.00 0.00 2.69
551 581 8.408043 AAATGTGTCATTAGTCCAGAAATTCA 57.592 30.769 0.00 0.00 0.00 2.57
552 582 8.514594 TGAAATGTGTCATTAGTCCAGAAATTC 58.485 33.333 0.00 0.00 0.00 2.17
553 583 8.299570 GTGAAATGTGTCATTAGTCCAGAAATT 58.700 33.333 0.00 0.00 0.00 1.82
559 589 6.114187 AGAGTGAAATGTGTCATTAGTCCA 57.886 37.500 0.00 0.00 0.00 4.02
561 591 8.534333 TTGTAGAGTGAAATGTGTCATTAGTC 57.466 34.615 0.00 0.00 0.00 2.59
562 592 7.118390 GCTTGTAGAGTGAAATGTGTCATTAGT 59.882 37.037 0.00 0.00 0.00 2.24
563 593 7.332926 AGCTTGTAGAGTGAAATGTGTCATTAG 59.667 37.037 0.00 0.00 0.00 1.73
587 617 4.207841 GCAAACTTGTTGAAACTCATGAGC 59.792 41.667 22.83 7.24 0.00 4.26
588 618 5.585390 AGCAAACTTGTTGAAACTCATGAG 58.415 37.500 21.37 21.37 0.00 2.90
589 619 5.450412 GGAGCAAACTTGTTGAAACTCATGA 60.450 40.000 0.00 0.00 0.00 3.07
591 621 4.498009 CGGAGCAAACTTGTTGAAACTCAT 60.498 41.667 0.00 0.00 0.00 2.90
592 622 3.181501 CGGAGCAAACTTGTTGAAACTCA 60.182 43.478 0.00 0.00 0.00 3.41
609 639 2.875684 GACCTTCGTCTGAGCGGAGC 62.876 65.000 0.02 0.00 45.47 4.70
617 647 1.153939 CGCCTCTGACCTTCGTCTG 60.154 63.158 0.00 0.00 39.94 3.51
621 651 0.734253 CAAGTCGCCTCTGACCTTCG 60.734 60.000 0.00 0.00 39.77 3.79
628 658 1.078759 CCGTAAGCAAGTCGCCTCTG 61.079 60.000 0.00 0.00 44.04 3.35
668 698 3.586892 GGTACCAAAGTCTTCTTCCTCG 58.413 50.000 7.15 0.00 32.90 4.63
722 752 8.972458 AAGCAAACAAACCCTTATAAAAACAT 57.028 26.923 0.00 0.00 0.00 2.71
843 873 4.988716 AGGACACGGGCAGGACGA 62.989 66.667 0.00 0.00 34.93 4.20
848 878 1.810532 GTCTAGAGGACACGGGCAG 59.189 63.158 0.00 0.00 43.94 4.85
1155 1185 1.289109 CGGTGGACTTGTTGTAGCCG 61.289 60.000 0.00 0.00 33.52 5.52
1251 1281 1.516603 GCCGTAGTCCTCGTTGCTC 60.517 63.158 0.00 0.00 0.00 4.26
1332 1362 1.786582 GCTGTACTCGTCGTCGTCT 59.213 57.895 1.33 0.00 38.33 4.18
1418 1493 2.276493 CGCTGTACTCGTCGTCGG 60.276 66.667 1.55 0.00 37.69 4.79
1474 1549 4.065281 GTCCCTGGACGACCCGTG 62.065 72.222 0.34 0.00 41.37 4.94
1610 1688 1.398390 AGCCTAAAATCTTTGCGCGAG 59.602 47.619 12.10 3.17 0.00 5.03
1620 1698 2.029365 GTGCGTTCGAGAGCCTAAAATC 59.971 50.000 10.91 0.00 0.00 2.17
1630 1708 1.066093 TGGAAACGTGCGTTCGAGA 59.934 52.632 10.46 0.00 37.35 4.04
1662 1740 2.357637 CCCGTTAATTCGCACCATCATT 59.642 45.455 0.00 0.00 0.00 2.57
1663 1741 1.946768 CCCGTTAATTCGCACCATCAT 59.053 47.619 0.00 0.00 0.00 2.45
1664 1742 1.374560 CCCGTTAATTCGCACCATCA 58.625 50.000 0.00 0.00 0.00 3.07
1665 1743 0.028902 GCCCGTTAATTCGCACCATC 59.971 55.000 0.00 0.00 0.00 3.51
1752 1832 1.006043 ACCTCCTCCTCGATCTTGTGA 59.994 52.381 0.00 0.00 0.00 3.58
1959 2039 0.316772 CGCGTATACGTGTGCTAGCT 60.317 55.000 26.58 0.00 44.02 3.32
1960 2040 2.122321 CGCGTATACGTGTGCTAGC 58.878 57.895 26.58 8.10 44.02 3.42
2079 2423 1.153066 AACACACGCACACCCATGA 60.153 52.632 0.00 0.00 0.00 3.07
2104 2448 4.325028 ACATACTCCACACAACGTTGTA 57.675 40.909 31.86 16.65 39.91 2.41
2105 2449 3.188159 ACATACTCCACACAACGTTGT 57.812 42.857 27.70 27.70 43.36 3.32
2106 2450 5.856126 AATACATACTCCACACAACGTTG 57.144 39.130 26.20 26.20 0.00 4.10
2107 2451 7.658575 AGTTAAATACATACTCCACACAACGTT 59.341 33.333 0.00 0.00 0.00 3.99
2108 2452 7.156673 AGTTAAATACATACTCCACACAACGT 58.843 34.615 0.00 0.00 0.00 3.99
2110 2454 7.749126 GCAAGTTAAATACATACTCCACACAAC 59.251 37.037 0.00 0.00 0.00 3.32
2111 2455 7.663905 AGCAAGTTAAATACATACTCCACACAA 59.336 33.333 0.00 0.00 0.00 3.33
2112 2456 7.119116 CAGCAAGTTAAATACATACTCCACACA 59.881 37.037 0.00 0.00 0.00 3.72
2120 2565 5.864986 ACACGCAGCAAGTTAAATACATAC 58.135 37.500 0.00 0.00 0.00 2.39
2154 2599 9.289782 AGACAAATATTTAGAAACAGAGCAAGT 57.710 29.630 0.00 0.00 0.00 3.16
2155 2600 9.766277 GAGACAAATATTTAGAAACAGAGCAAG 57.234 33.333 0.00 0.00 0.00 4.01
2156 2601 9.507329 AGAGACAAATATTTAGAAACAGAGCAA 57.493 29.630 0.00 0.00 0.00 3.91
2189 2634 8.493547 GCTTCGTAAGTAGTCACTTGTTAAAAT 58.506 33.333 0.35 0.00 44.81 1.82
2190 2635 7.492020 TGCTTCGTAAGTAGTCACTTGTTAAAA 59.508 33.333 0.35 0.00 44.81 1.52
2191 2636 6.979817 TGCTTCGTAAGTAGTCACTTGTTAAA 59.020 34.615 0.35 0.00 44.81 1.52
2192 2637 6.506147 TGCTTCGTAAGTAGTCACTTGTTAA 58.494 36.000 0.35 0.00 44.81 2.01
2193 2638 6.075762 TGCTTCGTAAGTAGTCACTTGTTA 57.924 37.500 0.35 0.00 44.81 2.41
2194 2639 4.940463 TGCTTCGTAAGTAGTCACTTGTT 58.060 39.130 0.35 0.00 44.81 2.83
2195 2640 4.579454 TGCTTCGTAAGTAGTCACTTGT 57.421 40.909 0.35 0.00 44.81 3.16
2196 2641 5.900339 TTTGCTTCGTAAGTAGTCACTTG 57.100 39.130 0.35 0.00 44.81 3.16
2197 2642 6.704493 TCATTTTGCTTCGTAAGTAGTCACTT 59.296 34.615 0.00 0.00 46.77 3.16
2198 2643 6.220930 TCATTTTGCTTCGTAAGTAGTCACT 58.779 36.000 0.00 0.00 37.06 3.41
2199 2644 6.365247 TCTCATTTTGCTTCGTAAGTAGTCAC 59.635 38.462 0.00 0.00 37.06 3.67
2200 2645 6.452242 TCTCATTTTGCTTCGTAAGTAGTCA 58.548 36.000 0.00 0.00 37.06 3.41
2201 2646 6.946229 TCTCATTTTGCTTCGTAAGTAGTC 57.054 37.500 0.00 0.00 37.06 2.59
2202 2647 7.724305 TTTCTCATTTTGCTTCGTAAGTAGT 57.276 32.000 0.00 0.00 37.06 2.73
2203 2648 9.267096 GATTTTCTCATTTTGCTTCGTAAGTAG 57.733 33.333 0.00 0.00 37.86 2.57
2204 2649 8.999431 AGATTTTCTCATTTTGCTTCGTAAGTA 58.001 29.630 0.00 0.00 39.48 2.24
2205 2650 7.875971 AGATTTTCTCATTTTGCTTCGTAAGT 58.124 30.769 0.00 0.00 39.48 2.24
2206 2651 9.267096 GTAGATTTTCTCATTTTGCTTCGTAAG 57.733 33.333 0.00 0.00 0.00 2.34
2207 2652 8.779303 TGTAGATTTTCTCATTTTGCTTCGTAA 58.221 29.630 0.00 0.00 0.00 3.18
2208 2653 8.227791 GTGTAGATTTTCTCATTTTGCTTCGTA 58.772 33.333 0.00 0.00 0.00 3.43
2209 2654 7.041098 AGTGTAGATTTTCTCATTTTGCTTCGT 60.041 33.333 0.00 0.00 0.00 3.85
2210 2655 7.301054 AGTGTAGATTTTCTCATTTTGCTTCG 58.699 34.615 0.00 0.00 0.00 3.79
2211 2656 9.468532 AAAGTGTAGATTTTCTCATTTTGCTTC 57.531 29.630 0.00 0.00 0.00 3.86
2343 2789 7.881643 ACTGATTGAATTCTCGATACTATGC 57.118 36.000 7.05 0.00 0.00 3.14
2373 2820 2.919960 TTTCGTCACGCCCGGAAACA 62.920 55.000 0.73 0.00 0.00 2.83
2501 4376 9.060347 AGAATGCAATCATATAAATCGAACAGT 57.940 29.630 4.25 0.00 31.46 3.55
2551 4457 5.528043 TTTTAAGGAAATGCAGTGCAAGA 57.472 34.783 23.90 0.00 43.62 3.02
2582 4489 3.903714 TCTTTCCAAGAGATGTGAGTGGA 59.096 43.478 0.00 0.00 36.59 4.02
2605 4512 9.305925 CAATAAACTAGGCAAAAATGAGAATCC 57.694 33.333 0.00 0.00 0.00 3.01
2688 4597 4.645588 CCTACTAATCTTCCGAGAACCTGT 59.354 45.833 0.00 0.00 35.07 4.00
2697 4606 4.024218 CGTCACCTACCTACTAATCTTCCG 60.024 50.000 0.00 0.00 0.00 4.30
2720 4629 4.767409 AGGATAAGCCACTTTCAAAGGTTC 59.233 41.667 1.31 0.00 40.02 3.62
2774 4683 6.924612 TCTCAATGACATCAACCACAAAAATG 59.075 34.615 0.00 0.00 0.00 2.32
2779 4688 5.507817 GCTTTCTCAATGACATCAACCACAA 60.508 40.000 0.00 0.00 0.00 3.33
2785 4694 5.045651 TCCCTAGCTTTCTCAATGACATCAA 60.046 40.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.