Multiple sequence alignment - TraesCS5D01G056900

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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 TraesCS5D01G056900 chr5D 100.000 3101 0 0 1 3101 52401723 52398623 0.000000e+00 5727.0
1 TraesCS5D01G056900 chr5D 97.500 40 1 0 395 434 530379343 530379304 5.550000e-08 69.4
2 TraesCS5D01G056900 chr5D 79.381 97 13 7 2274 2366 52393162 52393069 9.290000e-06 62.1
3 TraesCS5D01G056900 chr5A 94.088 2402 80 20 432 2821 41498733 41496382 0.000000e+00 3592.0
4 TraesCS5D01G056900 chr5A 95.683 139 2 2 2946 3082 6212820 6212956 1.450000e-53 220.0
5 TraesCS5D01G056900 chr5A 90.566 159 9 4 242 399 543202798 543202645 4.050000e-49 206.0
6 TraesCS5D01G056900 chr5A 90.446 157 11 2 242 398 297614710 297614862 1.460000e-48 204.0
7 TraesCS5D01G056900 chr5A 89.809 157 11 3 242 398 41498885 41498734 2.440000e-46 196.0
8 TraesCS5D01G056900 chr5A 92.063 126 10 0 433 558 543202648 543202523 8.840000e-41 178.0
9 TraesCS5D01G056900 chr5A 90.909 121 9 1 242 362 677744369 677744251 8.900000e-36 161.0
10 TraesCS5D01G056900 chr5A 89.256 121 10 2 242 362 543601654 543601537 6.930000e-32 148.0
11 TraesCS5D01G056900 chr5A 89.381 113 7 2 2826 2938 41496342 41496235 1.500000e-28 137.0
12 TraesCS5D01G056900 chr5A 95.714 70 3 0 146 215 41498954 41498885 2.530000e-21 113.0
13 TraesCS5D01G056900 chr5A 95.122 41 2 0 105 145 543202998 543202958 7.180000e-07 65.8
14 TraesCS5D01G056900 chr5A 90.909 44 4 0 102 145 297614507 297614550 3.340000e-05 60.2
15 TraesCS5D01G056900 chr5A 90.698 43 4 0 2324 2366 41474733 41474691 1.200000e-04 58.4
16 TraesCS5D01G056900 chr5B 95.685 2225 80 10 433 2653 55551211 55548999 0.000000e+00 3563.0
17 TraesCS5D01G056900 chr5B 86.224 196 14 5 146 335 55551458 55551270 1.890000e-47 200.0
18 TraesCS5D01G056900 chr5B 75.466 322 51 17 2556 2867 55548996 55548693 6.980000e-27 132.0
19 TraesCS5D01G056900 chr5B 78.571 98 16 3 2272 2366 55538060 55537965 3.340000e-05 60.2
20 TraesCS5D01G056900 chr5B 80.000 80 13 2 2278 2354 55547429 55547350 4.320000e-04 56.5
21 TraesCS5D01G056900 chrUn 75.458 982 232 8 1130 2105 26989367 26988389 1.300000e-128 470.0
22 TraesCS5D01G056900 chrUn 75.100 1004 236 10 1112 2102 27045475 27046477 1.010000e-124 457.0
23 TraesCS5D01G056900 chr6A 72.838 983 240 16 1130 2105 47645285 47644323 8.350000e-81 311.0
24 TraesCS5D01G056900 chr6A 95.588 136 4 2 2951 3086 13356296 13356163 1.870000e-52 217.0
25 TraesCS5D01G056900 chr7B 98.438 128 0 2 2951 3078 643352220 643352095 1.120000e-54 224.0
26 TraesCS5D01G056900 chr7B 95.139 144 2 4 2946 3085 608203201 608203059 4.020000e-54 222.0
27 TraesCS5D01G056900 chr7A 97.015 134 2 1 2946 3077 71013142 71013275 1.120000e-54 224.0
28 TraesCS5D01G056900 chr7A 99.200 125 0 1 2951 3075 332425481 332425358 1.120000e-54 224.0
29 TraesCS5D01G056900 chr4A 95.105 143 2 4 2946 3086 660924194 660924333 1.450000e-53 220.0
30 TraesCS5D01G056900 chr4A 95.349 43 2 0 399 441 584275519 584275561 5.550000e-08 69.4
31 TraesCS5D01G056900 chr3A 98.413 126 0 1 2946 3069 529616204 529616329 1.450000e-53 220.0
32 TraesCS5D01G056900 chr3A 91.139 158 10 2 242 399 425749652 425749805 8.710000e-51 211.0
33 TraesCS5D01G056900 chr3A 91.270 126 11 0 433 558 425749802 425749927 4.110000e-39 172.0
34 TraesCS5D01G056900 chr2A 95.714 140 1 3 2946 3082 527913575 527913712 1.450000e-53 220.0
35 TraesCS5D01G056900 chr1A 91.139 158 10 2 242 399 370931698 370931851 8.710000e-51 211.0
36 TraesCS5D01G056900 chr1A 93.243 74 4 1 143 215 370931625 370931698 1.180000e-19 108.0
37 TraesCS5D01G056900 chr1A 95.238 42 1 1 402 442 49282672 49282713 7.180000e-07 65.8
38 TraesCS5D01G056900 chr3B 93.617 47 1 2 401 446 443358100 443358145 5.550000e-08 69.4
39 TraesCS5D01G056900 chr3B 90.196 51 4 1 397 446 556504548 556504598 7.180000e-07 65.8
40 TraesCS5D01G056900 chr4B 95.238 42 2 0 399 440 437940428 437940469 2.000000e-07 67.6
41 TraesCS5D01G056900 chr2B 95.238 42 2 0 399 440 281511083 281511042 2.000000e-07 67.6
42 TraesCS5D01G056900 chr1B 95.238 42 2 0 402 443 616907504 616907545 2.000000e-07 67.6
43 TraesCS5D01G056900 chr6B 87.500 56 5 2 381 434 654847673 654847728 2.580000e-06 63.9


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 TraesCS5D01G056900 chr5D 52398623 52401723 3100 True 5727.000 5727 100.00000 1 3101 1 chr5D.!!$R2 3100
1 TraesCS5D01G056900 chr5A 41496235 41498954 2719 True 1009.500 3592 92.24800 146 2938 4 chr5A.!!$R4 2792
2 TraesCS5D01G056900 chr5B 55547350 55551458 4108 True 987.875 3563 84.34375 146 2867 4 chr5B.!!$R2 2721
3 TraesCS5D01G056900 chrUn 26988389 26989367 978 True 470.000 470 75.45800 1130 2105 1 chrUn.!!$R1 975
4 TraesCS5D01G056900 chrUn 27045475 27046477 1002 False 457.000 457 75.10000 1112 2102 1 chrUn.!!$F1 990
5 TraesCS5D01G056900 chr6A 47644323 47645285 962 True 311.000 311 72.83800 1130 2105 1 chr6A.!!$R2 975

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
75 76 0.029433 GCCGATTTGCGAAGGGATTC 59.971 55.0 10.10 0.00 44.57 2.52 F
80 81 0.035598 TTTGCGAAGGGATTCGGTCA 59.964 50.0 11.83 0.42 44.01 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2019 1.162181 CGGACGCTGACCTCGGTATA 61.162 60.000 0.0 0.0 0.0 1.47 R
2179 2200 3.996150 ACTGCTCCACATCAAACAAAG 57.004 42.857 0.0 0.0 0.0 2.77 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
30 31 3.188786 GCGGCGAGCGAGATTTGT 61.189 61.111 12.98 0.00 35.41 2.83
31 32 2.740714 GCGGCGAGCGAGATTTGTT 61.741 57.895 12.98 0.00 35.41 2.83
32 33 1.787847 CGGCGAGCGAGATTTGTTT 59.212 52.632 0.00 0.00 0.00 2.83
33 34 0.165944 CGGCGAGCGAGATTTGTTTT 59.834 50.000 0.00 0.00 0.00 2.43
34 35 1.399727 CGGCGAGCGAGATTTGTTTTT 60.400 47.619 0.00 0.00 0.00 1.94
35 36 2.242564 GGCGAGCGAGATTTGTTTTTC 58.757 47.619 0.00 0.00 0.00 2.29
36 37 1.898709 GCGAGCGAGATTTGTTTTTCG 59.101 47.619 0.00 0.00 36.23 3.46
37 38 2.661979 GCGAGCGAGATTTGTTTTTCGT 60.662 45.455 0.00 0.00 35.61 3.85
38 39 3.541711 CGAGCGAGATTTGTTTTTCGTT 58.458 40.909 0.00 0.00 35.61 3.85
39 40 3.354920 CGAGCGAGATTTGTTTTTCGTTG 59.645 43.478 0.00 0.00 35.61 4.10
40 41 3.628017 AGCGAGATTTGTTTTTCGTTGG 58.372 40.909 0.00 0.00 35.61 3.77
41 42 3.314080 AGCGAGATTTGTTTTTCGTTGGA 59.686 39.130 0.00 0.00 35.61 3.53
42 43 4.023193 AGCGAGATTTGTTTTTCGTTGGAT 60.023 37.500 0.00 0.00 35.61 3.41
43 44 4.679654 GCGAGATTTGTTTTTCGTTGGATT 59.320 37.500 0.00 0.00 35.61 3.01
44 45 5.174943 GCGAGATTTGTTTTTCGTTGGATTT 59.825 36.000 0.00 0.00 35.61 2.17
45 46 6.571588 CGAGATTTGTTTTTCGTTGGATTTG 58.428 36.000 0.00 0.00 0.00 2.32
46 47 6.345723 CGAGATTTGTTTTTCGTTGGATTTGG 60.346 38.462 0.00 0.00 0.00 3.28
47 48 4.866682 TTTGTTTTTCGTTGGATTTGGC 57.133 36.364 0.00 0.00 0.00 4.52
48 49 3.810310 TGTTTTTCGTTGGATTTGGCT 57.190 38.095 0.00 0.00 0.00 4.75
49 50 3.452474 TGTTTTTCGTTGGATTTGGCTG 58.548 40.909 0.00 0.00 0.00 4.85
50 51 2.799978 GTTTTTCGTTGGATTTGGCTGG 59.200 45.455 0.00 0.00 0.00 4.85
51 52 0.316841 TTTCGTTGGATTTGGCTGGC 59.683 50.000 0.00 0.00 0.00 4.85
52 53 1.861542 TTCGTTGGATTTGGCTGGCG 61.862 55.000 0.00 0.00 0.00 5.69
53 54 2.125952 GTTGGATTTGGCTGGCGC 60.126 61.111 0.00 0.00 0.00 6.53
69 70 2.100991 GCCTGCCGATTTGCGAAG 59.899 61.111 0.00 0.00 44.57 3.79
70 71 2.793946 CCTGCCGATTTGCGAAGG 59.206 61.111 0.00 0.00 44.57 3.46
71 72 2.764314 CCTGCCGATTTGCGAAGGG 61.764 63.158 2.78 2.78 44.57 3.95
72 73 1.745115 CTGCCGATTTGCGAAGGGA 60.745 57.895 10.10 0.00 44.57 4.20
73 74 1.077787 TGCCGATTTGCGAAGGGAT 60.078 52.632 10.10 0.00 44.57 3.85
74 75 0.679640 TGCCGATTTGCGAAGGGATT 60.680 50.000 10.10 0.00 44.57 3.01
75 76 0.029433 GCCGATTTGCGAAGGGATTC 59.971 55.000 10.10 0.00 44.57 2.52
76 77 0.304705 CCGATTTGCGAAGGGATTCG 59.695 55.000 6.04 6.04 46.34 3.34
77 78 0.304705 CGATTTGCGAAGGGATTCGG 59.695 55.000 11.83 0.00 44.01 4.30
78 79 1.379527 GATTTGCGAAGGGATTCGGT 58.620 50.000 11.83 0.00 44.01 4.69
79 80 1.330829 GATTTGCGAAGGGATTCGGTC 59.669 52.381 11.83 0.00 44.01 4.79
80 81 0.035598 TTTGCGAAGGGATTCGGTCA 59.964 50.000 11.83 0.42 44.01 4.02
81 82 0.391130 TTGCGAAGGGATTCGGTCAG 60.391 55.000 11.83 0.00 44.01 3.51
82 83 1.254975 TGCGAAGGGATTCGGTCAGA 61.255 55.000 11.83 0.00 44.01 3.27
83 84 0.528684 GCGAAGGGATTCGGTCAGAG 60.529 60.000 11.83 0.00 44.01 3.35
84 85 0.528684 CGAAGGGATTCGGTCAGAGC 60.529 60.000 2.55 0.00 40.48 4.09
85 86 0.179070 GAAGGGATTCGGTCAGAGCC 60.179 60.000 0.00 0.00 0.00 4.70
86 87 0.909610 AAGGGATTCGGTCAGAGCCA 60.910 55.000 0.00 0.00 0.00 4.75
87 88 1.153349 GGGATTCGGTCAGAGCCAC 60.153 63.158 0.00 0.00 0.00 5.01
88 89 1.153349 GGATTCGGTCAGAGCCACC 60.153 63.158 0.00 0.00 0.00 4.61
89 90 1.596934 GATTCGGTCAGAGCCACCA 59.403 57.895 0.00 0.00 32.89 4.17
90 91 0.036388 GATTCGGTCAGAGCCACCAA 60.036 55.000 0.00 0.00 32.89 3.67
91 92 0.620556 ATTCGGTCAGAGCCACCAAT 59.379 50.000 0.00 0.00 32.89 3.16
92 93 0.036388 TTCGGTCAGAGCCACCAATC 60.036 55.000 0.00 0.00 32.89 2.67
93 94 1.811266 CGGTCAGAGCCACCAATCG 60.811 63.158 0.00 0.00 32.89 3.34
94 95 1.450312 GGTCAGAGCCACCAATCGG 60.450 63.158 0.00 0.00 33.63 4.18
95 96 1.596934 GTCAGAGCCACCAATCGGA 59.403 57.895 0.00 0.00 35.59 4.55
96 97 0.460987 GTCAGAGCCACCAATCGGAG 60.461 60.000 0.00 0.00 35.59 4.63
97 98 1.153289 CAGAGCCACCAATCGGAGG 60.153 63.158 0.00 0.00 45.46 4.30
98 99 2.190578 GAGCCACCAATCGGAGGG 59.809 66.667 0.00 0.00 43.03 4.30
99 100 2.285368 AGCCACCAATCGGAGGGA 60.285 61.111 5.58 0.00 43.03 4.20
100 101 2.190578 GCCACCAATCGGAGGGAG 59.809 66.667 5.58 0.00 43.03 4.30
101 102 2.670148 GCCACCAATCGGAGGGAGT 61.670 63.158 5.58 0.00 43.03 3.85
102 103 1.522569 CCACCAATCGGAGGGAGTC 59.477 63.158 5.58 0.00 39.29 3.36
103 104 1.141881 CACCAATCGGAGGGAGTCG 59.858 63.158 5.58 0.00 35.59 4.18
104 105 2.107141 CCAATCGGAGGGAGTCGC 59.893 66.667 0.00 0.00 0.00 5.19
105 106 2.427245 CCAATCGGAGGGAGTCGCT 61.427 63.158 9.87 9.87 0.00 4.93
106 107 1.107538 CCAATCGGAGGGAGTCGCTA 61.108 60.000 10.08 0.00 0.00 4.26
107 108 0.312416 CAATCGGAGGGAGTCGCTAG 59.688 60.000 10.08 7.67 0.00 3.42
108 109 0.824182 AATCGGAGGGAGTCGCTAGG 60.824 60.000 10.08 5.24 0.00 3.02
109 110 1.997256 ATCGGAGGGAGTCGCTAGGT 61.997 60.000 10.08 0.89 0.00 3.08
110 111 2.482333 CGGAGGGAGTCGCTAGGTG 61.482 68.421 10.08 0.00 0.00 4.00
111 112 2.128507 GGAGGGAGTCGCTAGGTGG 61.129 68.421 10.08 0.00 0.00 4.61
112 113 2.760385 AGGGAGTCGCTAGGTGGC 60.760 66.667 8.15 0.00 0.00 5.01
120 121 4.137872 GCTAGGTGGCGGCGTGTA 62.138 66.667 9.37 0.00 0.00 2.90
121 122 2.104331 CTAGGTGGCGGCGTGTAG 59.896 66.667 9.37 0.49 0.00 2.74
122 123 2.677524 TAGGTGGCGGCGTGTAGT 60.678 61.111 9.37 0.00 0.00 2.73
123 124 2.884087 CTAGGTGGCGGCGTGTAGTG 62.884 65.000 9.37 0.00 0.00 2.74
124 125 4.675029 GGTGGCGGCGTGTAGTGT 62.675 66.667 9.37 0.00 0.00 3.55
125 126 2.259204 GTGGCGGCGTGTAGTGTA 59.741 61.111 9.37 0.00 0.00 2.90
126 127 1.804326 GTGGCGGCGTGTAGTGTAG 60.804 63.158 9.37 0.00 0.00 2.74
127 128 2.202703 GGCGGCGTGTAGTGTAGG 60.203 66.667 9.37 0.00 0.00 3.18
128 129 2.202703 GCGGCGTGTAGTGTAGGG 60.203 66.667 9.37 0.00 0.00 3.53
129 130 2.998279 GCGGCGTGTAGTGTAGGGT 61.998 63.158 9.37 0.00 0.00 4.34
130 131 1.656818 GCGGCGTGTAGTGTAGGGTA 61.657 60.000 9.37 0.00 0.00 3.69
131 132 0.810648 CGGCGTGTAGTGTAGGGTAA 59.189 55.000 0.00 0.00 0.00 2.85
132 133 1.202222 CGGCGTGTAGTGTAGGGTAAG 60.202 57.143 0.00 0.00 0.00 2.34
133 134 1.135721 GGCGTGTAGTGTAGGGTAAGG 59.864 57.143 0.00 0.00 0.00 2.69
134 135 1.470458 GCGTGTAGTGTAGGGTAAGGC 60.470 57.143 0.00 0.00 0.00 4.35
135 136 1.202222 CGTGTAGTGTAGGGTAAGGCG 60.202 57.143 0.00 0.00 0.00 5.52
136 137 1.135721 GTGTAGTGTAGGGTAAGGCGG 59.864 57.143 0.00 0.00 0.00 6.13
137 138 1.272648 TGTAGTGTAGGGTAAGGCGGT 60.273 52.381 0.00 0.00 0.00 5.68
138 139 1.406898 GTAGTGTAGGGTAAGGCGGTC 59.593 57.143 0.00 0.00 0.00 4.79
139 140 0.040794 AGTGTAGGGTAAGGCGGTCT 59.959 55.000 0.00 0.00 0.00 3.85
140 141 0.459078 GTGTAGGGTAAGGCGGTCTC 59.541 60.000 0.00 0.00 0.00 3.36
141 142 0.333993 TGTAGGGTAAGGCGGTCTCT 59.666 55.000 0.00 0.00 0.00 3.10
142 143 1.031235 GTAGGGTAAGGCGGTCTCTC 58.969 60.000 0.00 0.00 0.00 3.20
143 144 0.924823 TAGGGTAAGGCGGTCTCTCT 59.075 55.000 0.00 0.00 0.00 3.10
144 145 0.041386 AGGGTAAGGCGGTCTCTCTT 59.959 55.000 0.00 0.00 0.00 2.85
181 182 1.217747 TAACATGGGGTGGGGATGCA 61.218 55.000 0.00 0.00 0.00 3.96
216 223 3.956199 ACCAAATTGGGCATACAGATGAG 59.044 43.478 17.27 0.00 43.37 2.90
217 224 4.209538 CCAAATTGGGCATACAGATGAGA 58.790 43.478 3.60 0.00 32.10 3.27
218 225 4.831155 CCAAATTGGGCATACAGATGAGAT 59.169 41.667 3.60 0.00 32.10 2.75
219 226 5.278808 CCAAATTGGGCATACAGATGAGATG 60.279 44.000 3.60 0.00 32.10 2.90
220 227 4.987963 ATTGGGCATACAGATGAGATGA 57.012 40.909 0.00 0.00 34.73 2.92
226 233 4.222366 GGCATACAGATGAGATGATCCTCA 59.778 45.833 4.41 4.41 46.02 3.86
289 296 2.095059 GGCTTGCCATCTTACTTGTGTG 60.095 50.000 6.79 0.00 0.00 3.82
353 360 4.551671 CCCATCAGGTATATAGGAGGGAG 58.448 52.174 9.91 0.46 35.81 4.30
377 384 0.117340 AGACTGCAAGGGGTCCTAGT 59.883 55.000 0.52 0.00 39.30 2.57
381 388 1.073923 CTGCAAGGGGTCCTAGTTGTT 59.926 52.381 0.00 0.00 31.13 2.83
382 389 1.497286 TGCAAGGGGTCCTAGTTGTTT 59.503 47.619 0.00 0.00 31.13 2.83
401 408 9.362151 AGTTGTTTTGGAATCTTAAATACTCCA 57.638 29.630 0.00 0.00 34.36 3.86
402 409 9.974980 GTTGTTTTGGAATCTTAAATACTCCAA 57.025 29.630 0.00 0.00 42.89 3.53
408 415 8.398878 TGGAATCTTAAATACTCCAAAAACGT 57.601 30.769 0.00 0.00 33.25 3.99
409 416 8.508875 TGGAATCTTAAATACTCCAAAAACGTC 58.491 33.333 0.00 0.00 33.25 4.34
410 417 7.966753 GGAATCTTAAATACTCCAAAAACGTCC 59.033 37.037 0.00 0.00 0.00 4.79
411 418 8.631480 AATCTTAAATACTCCAAAAACGTCCT 57.369 30.769 0.00 0.00 0.00 3.85
412 419 9.729281 AATCTTAAATACTCCAAAAACGTCCTA 57.271 29.630 0.00 0.00 0.00 2.94
413 420 9.901172 ATCTTAAATACTCCAAAAACGTCCTAT 57.099 29.630 0.00 0.00 0.00 2.57
420 427 9.720769 ATACTCCAAAAACGTCCTATATTATGG 57.279 33.333 0.00 0.00 0.00 2.74
421 428 6.996282 ACTCCAAAAACGTCCTATATTATGGG 59.004 38.462 0.00 0.00 0.00 4.00
422 429 7.139287 TCCAAAAACGTCCTATATTATGGGA 57.861 36.000 4.74 4.74 37.61 4.37
429 436 3.990369 TCCTATATTATGGGACGGAGGG 58.010 50.000 4.74 0.00 34.71 4.30
430 437 3.599240 TCCTATATTATGGGACGGAGGGA 59.401 47.826 4.74 0.00 34.71 4.20
455 462 5.751243 ACTTGTTTGTGTGGTTGATAGAC 57.249 39.130 0.00 0.00 0.00 2.59
462 469 2.835764 GTGTGGTTGATAGACAGGGGTA 59.164 50.000 0.00 0.00 0.00 3.69
476 483 2.092968 CAGGGGTAGCTATGCTGTTGAA 60.093 50.000 0.00 0.00 40.10 2.69
478 485 3.010138 AGGGGTAGCTATGCTGTTGAAAA 59.990 43.478 0.00 0.00 40.10 2.29
489 496 3.226347 GCTGTTGAAAATACACGAGCAC 58.774 45.455 0.00 0.00 0.00 4.40
548 555 4.449131 CTGTGACAATAGATGATGCTGGT 58.551 43.478 0.00 0.00 0.00 4.00
716 723 6.198966 GTGCATTTAAAGAACAAGTCAGTTGG 59.801 38.462 0.00 0.00 40.90 3.77
780 787 4.202030 CCCCATTCTACTTCGTAGACTGAC 60.202 50.000 17.63 0.00 43.68 3.51
943 952 0.537653 GAGTACTTGGGGCACTCTCC 59.462 60.000 0.00 0.00 36.57 3.71
961 970 2.955660 CTCCTATGCTTCTCCGAGACTT 59.044 50.000 0.00 0.00 0.00 3.01
1515 1533 1.362224 TGCCCTTCCTTGTAGAAGCT 58.638 50.000 0.00 0.00 41.65 3.74
1890 1911 2.159382 GACCGGGTGAAACATGACATT 58.841 47.619 3.30 0.00 39.98 2.71
1953 1974 5.111293 GGGGATAACATTTTTGACATGCTG 58.889 41.667 0.00 0.00 0.00 4.41
1998 2019 1.563410 CTCTTCAAGAAGATGGGGCCT 59.437 52.381 12.50 0.00 45.40 5.19
2179 2200 5.761234 TGTTGTTACTGTGGAAATAGGTGTC 59.239 40.000 0.00 0.00 0.00 3.67
2476 2507 5.656416 AGAGATACAGAGTTAGCTGCTCTTT 59.344 40.000 16.79 14.09 40.97 2.52
2488 2519 9.982651 AGTTAGCTGCTCTTTTTCGATTATATA 57.017 29.630 4.91 0.00 0.00 0.86
2534 2565 6.852420 TCTATGCCTAGTGTTACTTGAACT 57.148 37.500 0.00 0.00 38.98 3.01
2570 2601 5.975693 TTCCCTCATGGACAAATGTTTAC 57.024 39.130 0.00 0.00 45.11 2.01
2693 2838 4.385865 CCCCTGCCATTGGTGTACTATTTA 60.386 45.833 4.26 0.00 0.00 1.40
2751 2896 7.639113 TTTACTCCCTTAAAGTATTGGCATG 57.361 36.000 0.00 0.00 0.00 4.06
2752 2897 5.450818 ACTCCCTTAAAGTATTGGCATGA 57.549 39.130 0.00 0.00 0.00 3.07
2765 2910 2.401766 GCATGAGCACTTCACCCCG 61.402 63.158 0.00 0.00 38.99 5.73
2772 2917 0.741221 GCACTTCACCCCGTCATCTC 60.741 60.000 0.00 0.00 0.00 2.75
2773 2918 0.108138 CACTTCACCCCGTCATCTCC 60.108 60.000 0.00 0.00 0.00 3.71
2848 3032 6.773200 TGGACAACATAATACAGGAACAAACA 59.227 34.615 0.00 0.00 0.00 2.83
2849 3033 7.450014 TGGACAACATAATACAGGAACAAACAT 59.550 33.333 0.00 0.00 0.00 2.71
2938 3141 9.850628 GAGTTTCATTTGATTTTCAGATCATCA 57.149 29.630 0.00 0.00 36.05 3.07
2944 3147 9.581099 CATTTGATTTTCAGATCATCAATGTCA 57.419 29.630 6.32 0.00 36.91 3.58
2950 3153 6.373186 TTCAGATCATCAATGTCATCAAGC 57.627 37.500 0.00 0.00 0.00 4.01
2953 3156 4.822350 AGATCATCAATGTCATCAAGCTGG 59.178 41.667 0.00 0.00 0.00 4.85
2954 3157 4.224991 TCATCAATGTCATCAAGCTGGA 57.775 40.909 0.00 0.00 0.00 3.86
2956 3159 5.011586 TCATCAATGTCATCAAGCTGGAAA 58.988 37.500 0.00 0.00 0.00 3.13
2974 3177 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2975 3178 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2976 3179 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2977 3180 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2978 3181 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2979 3182 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2981 3184 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2982 3185 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2983 3186 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2985 3188 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2986 3189 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2987 3190 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2988 3191 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2989 3192 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2990 3193 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2991 3194 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2992 3195 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2993 3196 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2994 3197 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2995 3198 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2996 3199 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2997 3200 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2998 3201 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2999 3202 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
3000 3203 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
3001 3204 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
3002 3205 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
3003 3206 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
3004 3207 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
3005 3208 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
3006 3209 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
3007 3210 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
3008 3211 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
3009 3212 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
3014 3217 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3015 3218 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3016 3219 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3017 3220 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3018 3221 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3019 3222 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3020 3223 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3021 3224 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3022 3225 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
3023 3226 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
3024 3227 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
3025 3228 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
3026 3229 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
3027 3230 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
3028 3231 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3029 3232 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3030 3233 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3031 3234 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3032 3235 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3033 3236 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3058 3261 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
3059 3262 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
3060 3263 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
3061 3264 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
3062 3265 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
3063 3266 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
3064 3267 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
3065 3268 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
3066 3269 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
3067 3270 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
3092 3295 5.305139 TCATCAATGTCATCAAGCTTGTG 57.695 39.130 25.19 20.85 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.887568 AAATCTCGCTCGCCGCTG 60.888 61.111 0.00 0.00 36.73 5.18
12 13 2.887568 CAAATCTCGCTCGCCGCT 60.888 61.111 0.00 0.00 36.73 5.52
13 14 2.240612 AAACAAATCTCGCTCGCCGC 62.241 55.000 0.00 0.00 36.73 6.53
14 15 0.165944 AAAACAAATCTCGCTCGCCG 59.834 50.000 0.00 0.00 38.61 6.46
15 16 2.242564 GAAAAACAAATCTCGCTCGCC 58.757 47.619 0.00 0.00 0.00 5.54
16 17 1.898709 CGAAAAACAAATCTCGCTCGC 59.101 47.619 0.00 0.00 0.00 5.03
17 18 3.169207 ACGAAAAACAAATCTCGCTCG 57.831 42.857 0.00 0.00 34.70 5.03
18 19 3.664025 CCAACGAAAAACAAATCTCGCTC 59.336 43.478 0.00 0.00 34.70 5.03
19 20 3.314080 TCCAACGAAAAACAAATCTCGCT 59.686 39.130 0.00 0.00 34.70 4.93
20 21 3.623863 TCCAACGAAAAACAAATCTCGC 58.376 40.909 0.00 0.00 34.70 5.03
21 22 6.345723 CCAAATCCAACGAAAAACAAATCTCG 60.346 38.462 0.00 0.00 37.33 4.04
22 23 6.563939 GCCAAATCCAACGAAAAACAAATCTC 60.564 38.462 0.00 0.00 0.00 2.75
23 24 5.236263 GCCAAATCCAACGAAAAACAAATCT 59.764 36.000 0.00 0.00 0.00 2.40
24 25 5.236263 AGCCAAATCCAACGAAAAACAAATC 59.764 36.000 0.00 0.00 0.00 2.17
25 26 5.007528 CAGCCAAATCCAACGAAAAACAAAT 59.992 36.000 0.00 0.00 0.00 2.32
26 27 4.331168 CAGCCAAATCCAACGAAAAACAAA 59.669 37.500 0.00 0.00 0.00 2.83
27 28 3.868077 CAGCCAAATCCAACGAAAAACAA 59.132 39.130 0.00 0.00 0.00 2.83
28 29 3.452474 CAGCCAAATCCAACGAAAAACA 58.548 40.909 0.00 0.00 0.00 2.83
29 30 2.799978 CCAGCCAAATCCAACGAAAAAC 59.200 45.455 0.00 0.00 0.00 2.43
30 31 2.804933 GCCAGCCAAATCCAACGAAAAA 60.805 45.455 0.00 0.00 0.00 1.94
31 32 1.270041 GCCAGCCAAATCCAACGAAAA 60.270 47.619 0.00 0.00 0.00 2.29
32 33 0.316841 GCCAGCCAAATCCAACGAAA 59.683 50.000 0.00 0.00 0.00 3.46
33 34 1.861542 CGCCAGCCAAATCCAACGAA 61.862 55.000 0.00 0.00 0.00 3.85
34 35 2.331893 CGCCAGCCAAATCCAACGA 61.332 57.895 0.00 0.00 0.00 3.85
35 36 2.179018 CGCCAGCCAAATCCAACG 59.821 61.111 0.00 0.00 0.00 4.10
36 37 2.125952 GCGCCAGCCAAATCCAAC 60.126 61.111 0.00 0.00 37.42 3.77
52 53 2.100991 CTTCGCAAATCGGCAGGC 59.899 61.111 0.00 0.00 39.05 4.85
53 54 2.764314 CCCTTCGCAAATCGGCAGG 61.764 63.158 0.00 0.00 38.21 4.85
54 55 1.097547 ATCCCTTCGCAAATCGGCAG 61.098 55.000 0.00 0.00 39.05 4.85
55 56 0.679640 AATCCCTTCGCAAATCGGCA 60.680 50.000 0.00 0.00 39.05 5.69
56 57 0.029433 GAATCCCTTCGCAAATCGGC 59.971 55.000 0.00 0.00 39.05 5.54
57 58 0.304705 CGAATCCCTTCGCAAATCGG 59.695 55.000 0.00 0.00 46.76 4.18
58 59 3.806257 CGAATCCCTTCGCAAATCG 57.194 52.632 0.00 0.00 46.76 3.34
66 67 0.179070 GGCTCTGACCGAATCCCTTC 60.179 60.000 0.00 0.00 0.00 3.46
67 68 0.909610 TGGCTCTGACCGAATCCCTT 60.910 55.000 0.00 0.00 0.00 3.95
68 69 1.306141 TGGCTCTGACCGAATCCCT 60.306 57.895 0.00 0.00 0.00 4.20
69 70 1.153349 GTGGCTCTGACCGAATCCC 60.153 63.158 0.00 0.00 0.00 3.85
70 71 1.153349 GGTGGCTCTGACCGAATCC 60.153 63.158 0.00 0.00 0.00 3.01
71 72 0.036388 TTGGTGGCTCTGACCGAATC 60.036 55.000 0.00 0.00 36.12 2.52
72 73 0.620556 ATTGGTGGCTCTGACCGAAT 59.379 50.000 0.00 0.00 36.12 3.34
73 74 0.036388 GATTGGTGGCTCTGACCGAA 60.036 55.000 0.00 0.00 36.12 4.30
74 75 1.596934 GATTGGTGGCTCTGACCGA 59.403 57.895 0.00 0.00 36.12 4.69
75 76 1.811266 CGATTGGTGGCTCTGACCG 60.811 63.158 0.00 0.00 36.12 4.79
76 77 1.450312 CCGATTGGTGGCTCTGACC 60.450 63.158 0.00 0.00 0.00 4.02
77 78 0.460987 CTCCGATTGGTGGCTCTGAC 60.461 60.000 0.00 0.00 36.30 3.51
78 79 1.617018 CCTCCGATTGGTGGCTCTGA 61.617 60.000 7.17 0.00 41.75 3.27
79 80 1.153289 CCTCCGATTGGTGGCTCTG 60.153 63.158 7.17 0.00 41.75 3.35
80 81 2.370445 CCCTCCGATTGGTGGCTCT 61.370 63.158 13.96 0.00 45.81 4.09
81 82 2.190578 CCCTCCGATTGGTGGCTC 59.809 66.667 13.96 0.00 45.81 4.70
82 83 2.285368 TCCCTCCGATTGGTGGCT 60.285 61.111 13.96 0.00 45.81 4.75
83 84 2.190578 CTCCCTCCGATTGGTGGC 59.809 66.667 13.96 0.00 45.81 5.01
84 85 1.522569 GACTCCCTCCGATTGGTGG 59.477 63.158 12.62 12.62 46.57 4.61
85 86 1.141881 CGACTCCCTCCGATTGGTG 59.858 63.158 0.00 0.00 36.30 4.17
86 87 2.722201 GCGACTCCCTCCGATTGGT 61.722 63.158 0.00 0.00 36.30 3.67
87 88 1.107538 TAGCGACTCCCTCCGATTGG 61.108 60.000 0.00 0.00 0.00 3.16
88 89 0.312416 CTAGCGACTCCCTCCGATTG 59.688 60.000 0.00 0.00 0.00 2.67
89 90 0.824182 CCTAGCGACTCCCTCCGATT 60.824 60.000 0.00 0.00 0.00 3.34
90 91 1.228306 CCTAGCGACTCCCTCCGAT 60.228 63.158 0.00 0.00 0.00 4.18
91 92 2.192443 CCTAGCGACTCCCTCCGA 59.808 66.667 0.00 0.00 0.00 4.55
92 93 2.124236 ACCTAGCGACTCCCTCCG 60.124 66.667 0.00 0.00 0.00 4.63
93 94 2.128507 CCACCTAGCGACTCCCTCC 61.129 68.421 0.00 0.00 0.00 4.30
94 95 2.787567 GCCACCTAGCGACTCCCTC 61.788 68.421 0.00 0.00 0.00 4.30
95 96 2.760385 GCCACCTAGCGACTCCCT 60.760 66.667 0.00 0.00 0.00 4.20
103 104 4.137872 TACACGCCGCCACCTAGC 62.138 66.667 0.00 0.00 0.00 3.42
104 105 2.104331 CTACACGCCGCCACCTAG 59.896 66.667 0.00 0.00 0.00 3.02
105 106 2.677524 ACTACACGCCGCCACCTA 60.678 61.111 0.00 0.00 0.00 3.08
106 107 4.373116 CACTACACGCCGCCACCT 62.373 66.667 0.00 0.00 0.00 4.00
107 108 3.285523 TACACTACACGCCGCCACC 62.286 63.158 0.00 0.00 0.00 4.61
108 109 1.804326 CTACACTACACGCCGCCAC 60.804 63.158 0.00 0.00 0.00 5.01
109 110 2.569657 CTACACTACACGCCGCCA 59.430 61.111 0.00 0.00 0.00 5.69
110 111 2.202703 CCTACACTACACGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
111 112 1.656818 TACCCTACACTACACGCCGC 61.657 60.000 0.00 0.00 0.00 6.53
112 113 0.810648 TTACCCTACACTACACGCCG 59.189 55.000 0.00 0.00 0.00 6.46
113 114 1.135721 CCTTACCCTACACTACACGCC 59.864 57.143 0.00 0.00 0.00 5.68
114 115 1.470458 GCCTTACCCTACACTACACGC 60.470 57.143 0.00 0.00 0.00 5.34
115 116 1.202222 CGCCTTACCCTACACTACACG 60.202 57.143 0.00 0.00 0.00 4.49
116 117 1.135721 CCGCCTTACCCTACACTACAC 59.864 57.143 0.00 0.00 0.00 2.90
117 118 1.272648 ACCGCCTTACCCTACACTACA 60.273 52.381 0.00 0.00 0.00 2.74
118 119 1.406898 GACCGCCTTACCCTACACTAC 59.593 57.143 0.00 0.00 0.00 2.73
119 120 1.285962 AGACCGCCTTACCCTACACTA 59.714 52.381 0.00 0.00 0.00 2.74
120 121 0.040794 AGACCGCCTTACCCTACACT 59.959 55.000 0.00 0.00 0.00 3.55
121 122 0.459078 GAGACCGCCTTACCCTACAC 59.541 60.000 0.00 0.00 0.00 2.90
122 123 0.333993 AGAGACCGCCTTACCCTACA 59.666 55.000 0.00 0.00 0.00 2.74
123 124 1.031235 GAGAGACCGCCTTACCCTAC 58.969 60.000 0.00 0.00 0.00 3.18
124 125 0.924823 AGAGAGACCGCCTTACCCTA 59.075 55.000 0.00 0.00 0.00 3.53
125 126 0.041386 AAGAGAGACCGCCTTACCCT 59.959 55.000 0.00 0.00 0.00 4.34
126 127 0.903236 AAAGAGAGACCGCCTTACCC 59.097 55.000 0.00 0.00 0.00 3.69
127 128 2.347731 CAAAAGAGAGACCGCCTTACC 58.652 52.381 0.00 0.00 0.00 2.85
128 129 1.732809 GCAAAAGAGAGACCGCCTTAC 59.267 52.381 0.00 0.00 0.00 2.34
129 130 1.623811 AGCAAAAGAGAGACCGCCTTA 59.376 47.619 0.00 0.00 0.00 2.69
130 131 0.398318 AGCAAAAGAGAGACCGCCTT 59.602 50.000 0.00 0.00 0.00 4.35
131 132 0.398318 AAGCAAAAGAGAGACCGCCT 59.602 50.000 0.00 0.00 0.00 5.52
132 133 0.799393 GAAGCAAAAGAGAGACCGCC 59.201 55.000 0.00 0.00 0.00 6.13
133 134 1.462670 CAGAAGCAAAAGAGAGACCGC 59.537 52.381 0.00 0.00 0.00 5.68
134 135 3.032017 TCAGAAGCAAAAGAGAGACCG 57.968 47.619 0.00 0.00 0.00 4.79
135 136 4.999950 TCATTCAGAAGCAAAAGAGAGACC 59.000 41.667 0.00 0.00 0.00 3.85
136 137 6.403418 CCATCATTCAGAAGCAAAAGAGAGAC 60.403 42.308 0.00 0.00 0.00 3.36
137 138 5.646793 CCATCATTCAGAAGCAAAAGAGAGA 59.353 40.000 0.00 0.00 0.00 3.10
138 139 5.415077 ACCATCATTCAGAAGCAAAAGAGAG 59.585 40.000 0.00 0.00 0.00 3.20
139 140 5.319453 ACCATCATTCAGAAGCAAAAGAGA 58.681 37.500 0.00 0.00 0.00 3.10
140 141 5.640189 ACCATCATTCAGAAGCAAAAGAG 57.360 39.130 0.00 0.00 0.00 2.85
141 142 6.489700 TGTTACCATCATTCAGAAGCAAAAGA 59.510 34.615 0.00 0.00 0.00 2.52
142 143 6.680810 TGTTACCATCATTCAGAAGCAAAAG 58.319 36.000 0.00 0.00 0.00 2.27
143 144 6.647334 TGTTACCATCATTCAGAAGCAAAA 57.353 33.333 0.00 0.00 0.00 2.44
144 145 6.350361 CCATGTTACCATCATTCAGAAGCAAA 60.350 38.462 0.00 0.00 0.00 3.68
167 168 1.935400 AATCTGCATCCCCACCCCA 60.935 57.895 0.00 0.00 0.00 4.96
219 226 2.081161 ACCCCTGCCCATGAGGATC 61.081 63.158 0.00 0.00 38.24 3.36
220 227 2.045132 ACCCCTGCCCATGAGGAT 59.955 61.111 0.00 0.00 38.24 3.24
229 236 2.604382 AAATGCCACACCCCTGCC 60.604 61.111 0.00 0.00 0.00 4.85
289 296 7.778470 ACTCACAACTATTTCTATTAGCAGC 57.222 36.000 0.00 0.00 0.00 5.25
340 347 3.663136 AGTCTGGTGCTCCCTCCTATATA 59.337 47.826 1.59 0.00 0.00 0.86
353 360 2.674380 CCCCTTGCAGTCTGGTGC 60.674 66.667 1.14 0.00 44.27 5.01
382 389 8.852135 ACGTTTTTGGAGTATTTAAGATTCCAA 58.148 29.630 11.59 11.59 43.96 3.53
399 406 7.198306 GTCCCATAATATAGGACGTTTTTGG 57.802 40.000 2.27 0.00 40.65 3.28
407 414 3.705072 CCCTCCGTCCCATAATATAGGAC 59.295 52.174 7.65 7.65 45.49 3.85
408 415 3.599240 TCCCTCCGTCCCATAATATAGGA 59.401 47.826 0.00 0.00 0.00 2.94
409 416 3.961408 CTCCCTCCGTCCCATAATATAGG 59.039 52.174 0.00 0.00 0.00 2.57
410 417 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
411 418 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
412 419 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
413 420 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
414 421 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
415 422 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
416 423 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
417 424 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
418 425 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
419 426 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
420 427 1.264295 AACAAGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
421 428 2.036862 ACAAACAAGTACTCCCTCCGTC 59.963 50.000 0.00 0.00 0.00 4.79
422 429 2.044758 ACAAACAAGTACTCCCTCCGT 58.955 47.619 0.00 0.00 0.00 4.69
423 430 2.224209 ACACAAACAAGTACTCCCTCCG 60.224 50.000 0.00 0.00 0.00 4.63
424 431 3.139077 CACACAAACAAGTACTCCCTCC 58.861 50.000 0.00 0.00 0.00 4.30
425 432 3.139077 CCACACAAACAAGTACTCCCTC 58.861 50.000 0.00 0.00 0.00 4.30
426 433 2.508300 ACCACACAAACAAGTACTCCCT 59.492 45.455 0.00 0.00 0.00 4.20
427 434 2.927028 ACCACACAAACAAGTACTCCC 58.073 47.619 0.00 0.00 0.00 4.30
428 435 3.942748 TCAACCACACAAACAAGTACTCC 59.057 43.478 0.00 0.00 0.00 3.85
429 436 5.751243 ATCAACCACACAAACAAGTACTC 57.249 39.130 0.00 0.00 0.00 2.59
430 437 6.482308 GTCTATCAACCACACAAACAAGTACT 59.518 38.462 0.00 0.00 0.00 2.73
455 462 1.486310 TCAACAGCATAGCTACCCCTG 59.514 52.381 12.91 12.91 36.40 4.45
462 469 4.935205 TCGTGTATTTTCAACAGCATAGCT 59.065 37.500 0.00 0.00 40.77 3.32
476 483 5.235186 GCATGATCTAAGTGCTCGTGTATTT 59.765 40.000 0.00 0.00 36.02 1.40
478 485 4.038522 AGCATGATCTAAGTGCTCGTGTAT 59.961 41.667 0.00 0.00 45.42 2.29
489 496 3.624777 ACCCCAACAAGCATGATCTAAG 58.375 45.455 0.00 0.00 0.00 2.18
548 555 2.703416 CAGCATAACACCAGAGCAGAA 58.297 47.619 0.00 0.00 0.00 3.02
716 723 4.576463 ACAGACTCTTGTGAATTTGTGACC 59.424 41.667 0.00 0.00 0.00 4.02
815 822 4.634012 AAGTGGTACAGGAAGCAACATA 57.366 40.909 0.00 0.00 41.80 2.29
816 823 3.508845 AAGTGGTACAGGAAGCAACAT 57.491 42.857 0.00 0.00 41.80 2.71
817 824 3.118038 AGAAAGTGGTACAGGAAGCAACA 60.118 43.478 0.00 0.00 41.80 3.33
943 952 2.100584 AGCAAGTCTCGGAGAAGCATAG 59.899 50.000 22.26 8.25 34.09 2.23
961 970 2.596346 TGGCAAGGAAAGAAATGAGCA 58.404 42.857 0.00 0.00 0.00 4.26
1697 1715 3.446161 CCAGCTGTTTTGATCCACATGAT 59.554 43.478 13.81 0.00 36.01 2.45
1953 1974 2.230750 ACTAAACGTGTACTCCTCAGGC 59.769 50.000 0.00 0.00 0.00 4.85
1998 2019 1.162181 CGGACGCTGACCTCGGTATA 61.162 60.000 0.00 0.00 0.00 1.47
2179 2200 3.996150 ACTGCTCCACATCAAACAAAG 57.004 42.857 0.00 0.00 0.00 2.77
2476 2507 8.699749 CAAACGATGCAGAGTATATAATCGAAA 58.300 33.333 15.60 2.84 39.30 3.46
2551 2582 7.447374 TGTAAGTAAACATTTGTCCATGAGG 57.553 36.000 0.00 0.00 0.00 3.86
2665 2810 1.055040 CACCAATGGCAGGGGAAAAA 58.945 50.000 13.53 0.00 0.00 1.94
2666 2811 0.105246 ACACCAATGGCAGGGGAAAA 60.105 50.000 13.53 0.00 32.49 2.29
2667 2812 0.780637 TACACCAATGGCAGGGGAAA 59.219 50.000 13.53 0.00 32.49 3.13
2668 2813 0.039035 GTACACCAATGGCAGGGGAA 59.961 55.000 13.53 0.00 32.49 3.97
2669 2814 0.844661 AGTACACCAATGGCAGGGGA 60.845 55.000 13.53 0.00 32.49 4.81
2670 2815 0.916086 TAGTACACCAATGGCAGGGG 59.084 55.000 12.07 9.03 35.02 4.79
2671 2816 3.297134 AATAGTACACCAATGGCAGGG 57.703 47.619 0.00 6.45 0.00 4.45
2672 2817 5.827797 ACATAAATAGTACACCAATGGCAGG 59.172 40.000 0.00 0.00 0.00 4.85
2673 2818 6.942532 ACATAAATAGTACACCAATGGCAG 57.057 37.500 0.00 0.00 0.00 4.85
2674 2819 7.710676 AAACATAAATAGTACACCAATGGCA 57.289 32.000 0.00 0.00 0.00 4.92
2675 2820 7.704899 GGAAAACATAAATAGTACACCAATGGC 59.295 37.037 0.00 0.00 0.00 4.40
2676 2821 8.966868 AGGAAAACATAAATAGTACACCAATGG 58.033 33.333 0.00 0.00 0.00 3.16
2693 2838 6.527423 TCGTGTTCTAGGTTAAGGAAAACAT 58.473 36.000 0.00 0.00 30.19 2.71
2715 2860 7.619964 TTAAGGGAGTAAAATAGGCTTTTCG 57.380 36.000 0.00 0.00 0.00 3.46
2751 2896 0.741221 GATGACGGGGTGAAGTGCTC 60.741 60.000 0.00 0.00 0.00 4.26
2752 2897 1.194781 AGATGACGGGGTGAAGTGCT 61.195 55.000 0.00 0.00 0.00 4.40
2765 2910 0.537188 TTCCAAGCCTCGGAGATGAC 59.463 55.000 6.58 0.00 33.89 3.06
2772 2917 2.178912 TTTACAGTTCCAAGCCTCGG 57.821 50.000 0.00 0.00 0.00 4.63
2773 2918 2.420022 CCATTTACAGTTCCAAGCCTCG 59.580 50.000 0.00 0.00 0.00 4.63
2873 3058 7.940850 ACTGAATAATAATTATGCAAAGCGGT 58.059 30.769 0.00 0.00 30.87 5.68
2902 3105 4.133820 TCAAATGAAACTCTCTGCCGAAA 58.866 39.130 0.00 0.00 0.00 3.46
2906 3109 6.449698 TGAAAATCAAATGAAACTCTCTGCC 58.550 36.000 0.00 0.00 0.00 4.85
2938 3141 4.778534 CTGTTTCCAGCTTGATGACATT 57.221 40.909 5.38 0.00 0.00 2.71
2950 3153 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2962 3165 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2963 3166 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2964 3167 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2965 3168 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2966 3169 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2969 3172 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2971 3174 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2974 3177 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2975 3178 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2976 3179 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2977 3180 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2978 3181 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2979 3182 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2981 3184 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2982 3185 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2983 3186 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2985 3188 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2986 3189 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2987 3190 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2988 3191 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2998 3201 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2999 3202 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3000 3203 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3001 3204 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3002 3205 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3003 3206 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3004 3207 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3005 3208 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
3006 3209 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
3007 3210 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3008 3211 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3009 3212 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3010 3213 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3011 3214 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3012 3215 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3013 3216 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3014 3217 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
3015 3218 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
3016 3219 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
3028 3231 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3031 3234 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3032 3235 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3033 3236 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3034 3237 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3040 3243 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
3041 3244 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
3042 3245 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
3043 3246 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
3044 3247 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
3064 3267 9.361315 CAAGCTTGATGACATTGATGATAAAAA 57.639 29.630 22.31 0.00 0.00 1.94
3065 3268 8.525316 ACAAGCTTGATGACATTGATGATAAAA 58.475 29.630 32.50 0.00 0.00 1.52
3066 3269 7.971722 CACAAGCTTGATGACATTGATGATAAA 59.028 33.333 32.50 0.00 0.00 1.40
3067 3270 7.477494 CACAAGCTTGATGACATTGATGATAA 58.523 34.615 32.50 0.00 0.00 1.75
3068 3271 6.459161 GCACAAGCTTGATGACATTGATGATA 60.459 38.462 32.50 0.00 37.91 2.15
3069 3272 5.678871 GCACAAGCTTGATGACATTGATGAT 60.679 40.000 32.50 1.82 37.91 2.45
3070 3273 4.380128 GCACAAGCTTGATGACATTGATGA 60.380 41.667 32.50 0.00 37.91 2.92
3071 3274 3.857665 GCACAAGCTTGATGACATTGATG 59.142 43.478 32.50 16.38 37.91 3.07
3072 3275 4.106029 GCACAAGCTTGATGACATTGAT 57.894 40.909 32.50 3.08 37.91 2.57
3073 3276 3.564235 GCACAAGCTTGATGACATTGA 57.436 42.857 32.50 0.00 37.91 2.57


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

AutoCloner maintained by Alex Coulton.