Multiple sequence alignment - TraesCS2A01G415100

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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 TraesCS2A01G415100 chr2A 100.000 2645 0 0 1 2645 672235990 672233346 0.000000e+00 4885.0
1 TraesCS2A01G415100 chr2A 88.552 297 27 6 1080 1371 672265712 672265418 1.160000e-93 353.0
2 TraesCS2A01G415100 chr2B 89.639 2355 127 47 320 2594 623870801 623868484 0.000000e+00 2889.0
3 TraesCS2A01G415100 chr2B 87.879 297 29 5 1080 1371 624287336 624287042 2.520000e-90 342.0
4 TraesCS2A01G415100 chr2D 91.063 2182 114 44 490 2637 527004837 527002703 0.000000e+00 2874.0
5 TraesCS2A01G415100 chr2D 89.078 293 29 2 1082 1371 527272592 527272300 6.960000e-96 361.0
6 TraesCS2A01G415100 chr2D 90.164 183 14 2 320 502 527005064 527004886 4.400000e-58 235.0
7 TraesCS2A01G415100 chr2D 80.734 109 20 1 213 321 159579054 159578947 1.690000e-12 84.2
8 TraesCS2A01G415100 chr6A 81.017 590 74 23 1081 1643 465389750 465390328 4.040000e-118 435.0
9 TraesCS2A01G415100 chr6A 88.353 249 23 3 1117 1359 465316702 465316950 7.160000e-76 294.0
10 TraesCS2A01G415100 chr6A 89.937 159 16 0 42 200 70548836 70548678 3.450000e-49 206.0
11 TraesCS2A01G415100 chr6D 80.895 581 79 23 1081 1643 326760674 326761240 1.880000e-116 429.0
12 TraesCS2A01G415100 chr6D 84.444 90 13 1 232 321 34399134 34399222 1.300000e-13 87.9
13 TraesCS2A01G415100 chr6B 80.369 596 79 22 1081 1643 495543810 495543220 4.070000e-113 418.0
14 TraesCS2A01G415100 chr6B 80.808 99 17 2 223 321 10232673 10232769 2.820000e-10 76.8
15 TraesCS2A01G415100 chr7D 92.453 159 12 0 42 200 292249467 292249625 7.370000e-56 228.0
16 TraesCS2A01G415100 chr7D 91.824 159 13 0 42 200 506903998 506903840 3.430000e-54 222.0
17 TraesCS2A01G415100 chr1D 91.824 159 13 0 42 200 225540504 225540346 3.430000e-54 222.0
18 TraesCS2A01G415100 chr5B 91.195 159 14 0 42 200 522838541 522838383 1.590000e-52 217.0
19 TraesCS2A01G415100 chr5B 79.279 111 21 2 212 321 466843447 466843556 2.820000e-10 76.8
20 TraesCS2A01G415100 chr3D 90.566 159 15 0 42 200 441402532 441402374 7.420000e-51 211.0
21 TraesCS2A01G415100 chr7A 89.308 159 17 0 42 200 55435824 55435666 1.610000e-47 200.0
22 TraesCS2A01G415100 chr7A 86.957 92 11 1 218 308 584097355 584097446 4.660000e-18 102.0
23 TraesCS2A01G415100 chr1B 85.535 159 23 0 42 200 178654581 178654423 1.630000e-37 167.0
24 TraesCS2A01G415100 chr1B 82.075 106 15 4 218 321 138560292 138560395 1.300000e-13 87.9
25 TraesCS2A01G415100 chr5D 83.784 111 16 2 212 321 459220252 459220143 1.300000e-18 104.0
26 TraesCS2A01G415100 chr3B 84.884 86 9 4 223 308 117708113 117708032 1.690000e-12 84.2
27 TraesCS2A01G415100 chrUn 81.633 98 17 1 212 309 46187189 46187093 2.180000e-11 80.5
28 TraesCS2A01G415100 chr5A 82.105 95 11 3 1338 1432 8111600 8111512 2.820000e-10 76.8


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 TraesCS2A01G415100 chr2A 672233346 672235990 2644 True 4885.0 4885 100.0000 1 2645 1 chr2A.!!$R1 2644
1 TraesCS2A01G415100 chr2B 623868484 623870801 2317 True 2889.0 2889 89.6390 320 2594 1 chr2B.!!$R1 2274
2 TraesCS2A01G415100 chr2D 527002703 527005064 2361 True 1554.5 2874 90.6135 320 2637 2 chr2D.!!$R3 2317
3 TraesCS2A01G415100 chr6A 465389750 465390328 578 False 435.0 435 81.0170 1081 1643 1 chr6A.!!$F2 562
4 TraesCS2A01G415100 chr6D 326760674 326761240 566 False 429.0 429 80.8950 1081 1643 1 chr6D.!!$F2 562
5 TraesCS2A01G415100 chr6B 495543220 495543810 590 True 418.0 418 80.3690 1081 1643 1 chr6B.!!$R1 562

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
40 41 0.106149 AGTGGTCGTTTGGTGGTCTC 59.894 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2111 0.171903 CCCAAATCAAGCAAGGCGAG 59.828 55.0 0.0 0.0 0.0 5.03 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
17 18 3.805267 CCGGCTCATTCTGACAGC 58.195 61.111 0.00 0.00 0.00 4.40
18 19 2.169789 CCGGCTCATTCTGACAGCG 61.170 63.158 0.00 0.00 0.00 5.18
19 20 2.169789 CGGCTCATTCTGACAGCGG 61.170 63.158 0.00 0.00 0.00 5.52
20 21 1.078848 GGCTCATTCTGACAGCGGT 60.079 57.895 0.00 0.00 0.00 5.68
21 22 0.175760 GGCTCATTCTGACAGCGGTA 59.824 55.000 0.00 0.00 0.00 4.02
22 23 1.565305 GCTCATTCTGACAGCGGTAG 58.435 55.000 0.00 0.00 0.00 3.18
23 24 1.134965 GCTCATTCTGACAGCGGTAGT 60.135 52.381 0.00 0.00 0.00 2.73
24 25 2.534298 CTCATTCTGACAGCGGTAGTG 58.466 52.381 0.00 0.00 0.00 2.74
25 26 1.204704 TCATTCTGACAGCGGTAGTGG 59.795 52.381 0.00 0.00 0.00 4.00
26 27 1.066858 CATTCTGACAGCGGTAGTGGT 60.067 52.381 0.00 0.00 0.00 4.16
27 28 0.601558 TTCTGACAGCGGTAGTGGTC 59.398 55.000 0.00 0.00 0.00 4.02
28 29 1.154016 CTGACAGCGGTAGTGGTCG 60.154 63.158 0.00 0.00 33.04 4.79
29 30 1.863662 CTGACAGCGGTAGTGGTCGT 61.864 60.000 0.00 0.00 33.04 4.34
30 31 1.288127 GACAGCGGTAGTGGTCGTT 59.712 57.895 0.00 0.00 0.00 3.85
31 32 0.319297 GACAGCGGTAGTGGTCGTTT 60.319 55.000 0.00 0.00 0.00 3.60
32 33 0.599204 ACAGCGGTAGTGGTCGTTTG 60.599 55.000 0.00 0.00 0.00 2.93
33 34 1.005394 AGCGGTAGTGGTCGTTTGG 60.005 57.895 0.00 0.00 0.00 3.28
34 35 1.301165 GCGGTAGTGGTCGTTTGGT 60.301 57.895 0.00 0.00 0.00 3.67
35 36 1.562575 GCGGTAGTGGTCGTTTGGTG 61.563 60.000 0.00 0.00 0.00 4.17
36 37 0.947180 CGGTAGTGGTCGTTTGGTGG 60.947 60.000 0.00 0.00 0.00 4.61
37 38 0.107268 GGTAGTGGTCGTTTGGTGGT 59.893 55.000 0.00 0.00 0.00 4.16
38 39 1.505425 GTAGTGGTCGTTTGGTGGTC 58.495 55.000 0.00 0.00 0.00 4.02
39 40 1.069668 GTAGTGGTCGTTTGGTGGTCT 59.930 52.381 0.00 0.00 0.00 3.85
40 41 0.106149 AGTGGTCGTTTGGTGGTCTC 59.894 55.000 0.00 0.00 0.00 3.36
41 42 0.106149 GTGGTCGTTTGGTGGTCTCT 59.894 55.000 0.00 0.00 0.00 3.10
42 43 0.834612 TGGTCGTTTGGTGGTCTCTT 59.165 50.000 0.00 0.00 0.00 2.85
43 44 1.210967 TGGTCGTTTGGTGGTCTCTTT 59.789 47.619 0.00 0.00 0.00 2.52
44 45 2.294979 GGTCGTTTGGTGGTCTCTTTT 58.705 47.619 0.00 0.00 0.00 2.27
45 46 2.686405 GGTCGTTTGGTGGTCTCTTTTT 59.314 45.455 0.00 0.00 0.00 1.94
64 65 5.993748 TTTTTGCGGGATAAAGGAAGATT 57.006 34.783 0.00 0.00 0.00 2.40
65 66 5.993748 TTTTGCGGGATAAAGGAAGATTT 57.006 34.783 0.00 0.00 0.00 2.17
66 67 5.576447 TTTGCGGGATAAAGGAAGATTTC 57.424 39.130 0.00 0.00 0.00 2.17
67 68 4.229304 TGCGGGATAAAGGAAGATTTCA 57.771 40.909 0.00 0.00 0.00 2.69
68 69 4.792068 TGCGGGATAAAGGAAGATTTCAT 58.208 39.130 0.00 0.00 0.00 2.57
69 70 5.200483 TGCGGGATAAAGGAAGATTTCATT 58.800 37.500 0.00 0.00 34.80 2.57
70 71 5.299279 TGCGGGATAAAGGAAGATTTCATTC 59.701 40.000 0.00 0.00 31.69 2.67
71 72 5.299279 GCGGGATAAAGGAAGATTTCATTCA 59.701 40.000 0.00 0.00 31.69 2.57
72 73 6.015940 GCGGGATAAAGGAAGATTTCATTCAT 60.016 38.462 0.00 0.00 31.69 2.57
73 74 7.470563 GCGGGATAAAGGAAGATTTCATTCATT 60.471 37.037 0.00 0.00 31.69 2.57
74 75 8.078596 CGGGATAAAGGAAGATTTCATTCATTC 58.921 37.037 0.00 0.00 31.69 2.67
75 76 8.917088 GGGATAAAGGAAGATTTCATTCATTCA 58.083 33.333 0.00 0.00 31.69 2.57
78 79 9.793252 ATAAAGGAAGATTTCATTCATTCAACG 57.207 29.630 0.00 0.00 31.69 4.10
79 80 7.452880 AAGGAAGATTTCATTCATTCAACGA 57.547 32.000 0.00 0.00 0.00 3.85
80 81 7.081526 AGGAAGATTTCATTCATTCAACGAG 57.918 36.000 0.00 0.00 0.00 4.18
81 82 6.094603 AGGAAGATTTCATTCATTCAACGAGG 59.905 38.462 0.00 0.00 0.00 4.63
82 83 5.240713 AGATTTCATTCATTCAACGAGGC 57.759 39.130 0.00 0.00 0.00 4.70
83 84 4.946157 AGATTTCATTCATTCAACGAGGCT 59.054 37.500 0.00 0.00 0.00 4.58
84 85 5.416952 AGATTTCATTCATTCAACGAGGCTT 59.583 36.000 0.00 0.00 0.00 4.35
85 86 4.685169 TTCATTCATTCAACGAGGCTTC 57.315 40.909 0.00 0.00 0.00 3.86
86 87 3.942829 TCATTCATTCAACGAGGCTTCT 58.057 40.909 0.00 0.00 0.00 2.85
87 88 3.935203 TCATTCATTCAACGAGGCTTCTC 59.065 43.478 0.00 0.00 0.00 2.87
99 100 2.761071 GCTTCTCGGCCTCTGAAAG 58.239 57.895 0.00 0.00 0.00 2.62
110 111 3.565905 CCTCTGAAAGGTTCACAATGC 57.434 47.619 0.00 0.00 40.67 3.56
111 112 2.886523 CCTCTGAAAGGTTCACAATGCA 59.113 45.455 0.00 0.00 40.67 3.96
112 113 3.057736 CCTCTGAAAGGTTCACAATGCAG 60.058 47.826 0.00 0.00 40.67 4.41
113 114 3.554934 TCTGAAAGGTTCACAATGCAGT 58.445 40.909 0.00 0.00 35.46 4.40
114 115 3.565482 TCTGAAAGGTTCACAATGCAGTC 59.435 43.478 0.00 0.00 35.46 3.51
115 116 3.554934 TGAAAGGTTCACAATGCAGTCT 58.445 40.909 0.00 0.00 34.08 3.24
116 117 4.713553 TGAAAGGTTCACAATGCAGTCTA 58.286 39.130 0.00 0.00 34.08 2.59
117 118 5.129634 TGAAAGGTTCACAATGCAGTCTAA 58.870 37.500 0.00 0.00 34.08 2.10
118 119 5.769662 TGAAAGGTTCACAATGCAGTCTAAT 59.230 36.000 0.00 0.00 34.08 1.73
119 120 5.886960 AAGGTTCACAATGCAGTCTAATC 57.113 39.130 0.00 0.00 0.00 1.75
120 121 4.265073 AGGTTCACAATGCAGTCTAATCC 58.735 43.478 0.00 0.00 0.00 3.01
121 122 3.378427 GGTTCACAATGCAGTCTAATCCC 59.622 47.826 0.00 0.00 0.00 3.85
122 123 2.905075 TCACAATGCAGTCTAATCCCG 58.095 47.619 0.00 0.00 0.00 5.14
123 124 2.499693 TCACAATGCAGTCTAATCCCGA 59.500 45.455 0.00 0.00 0.00 5.14
124 125 3.134623 TCACAATGCAGTCTAATCCCGAT 59.865 43.478 0.00 0.00 0.00 4.18
125 126 3.496130 CACAATGCAGTCTAATCCCGATC 59.504 47.826 0.00 0.00 0.00 3.69
126 127 2.732412 ATGCAGTCTAATCCCGATCG 57.268 50.000 8.51 8.51 0.00 3.69
127 128 1.399714 TGCAGTCTAATCCCGATCGT 58.600 50.000 15.09 0.00 0.00 3.73
128 129 1.067060 TGCAGTCTAATCCCGATCGTG 59.933 52.381 15.09 1.95 0.00 4.35
129 130 1.337071 GCAGTCTAATCCCGATCGTGA 59.663 52.381 15.09 8.85 0.00 4.35
130 131 2.859032 GCAGTCTAATCCCGATCGTGAC 60.859 54.545 15.09 11.33 0.00 3.67
131 132 1.955080 AGTCTAATCCCGATCGTGACC 59.045 52.381 15.09 0.00 0.00 4.02
132 133 1.679680 GTCTAATCCCGATCGTGACCA 59.320 52.381 15.09 0.00 0.00 4.02
133 134 1.679680 TCTAATCCCGATCGTGACCAC 59.320 52.381 15.09 0.00 0.00 4.16
134 135 1.407618 CTAATCCCGATCGTGACCACA 59.592 52.381 15.09 0.00 0.00 4.17
135 136 0.108329 AATCCCGATCGTGACCACAC 60.108 55.000 15.09 0.00 42.88 3.82
136 137 1.254975 ATCCCGATCGTGACCACACA 61.255 55.000 15.09 0.00 46.20 3.72
137 138 1.446099 CCCGATCGTGACCACACAG 60.446 63.158 15.09 0.00 46.20 3.66
138 139 2.094659 CCGATCGTGACCACACAGC 61.095 63.158 15.09 0.00 46.20 4.40
139 140 2.094659 CGATCGTGACCACACAGCC 61.095 63.158 7.03 0.00 46.20 4.85
140 141 2.048222 ATCGTGACCACACAGCCG 60.048 61.111 0.00 0.00 46.20 5.52
141 142 2.765250 GATCGTGACCACACAGCCGT 62.765 60.000 0.00 0.00 46.20 5.68
156 157 2.724721 CGTGCGCGGGATACTACG 60.725 66.667 12.87 0.00 37.80 3.51
157 158 2.410469 GTGCGCGGGATACTACGT 59.590 61.111 8.83 0.00 37.23 3.57
158 159 1.656569 GTGCGCGGGATACTACGTC 60.657 63.158 8.83 0.00 37.23 4.34
159 160 2.050623 GCGCGGGATACTACGTCC 60.051 66.667 8.83 0.00 37.23 4.79
160 161 2.837883 GCGCGGGATACTACGTCCA 61.838 63.158 8.83 0.00 37.49 4.02
161 162 1.954528 CGCGGGATACTACGTCCAT 59.045 57.895 0.00 0.00 37.49 3.41
162 163 1.159285 CGCGGGATACTACGTCCATA 58.841 55.000 0.00 0.00 37.49 2.74
163 164 1.135859 CGCGGGATACTACGTCCATAC 60.136 57.143 0.00 0.00 37.49 2.39
172 173 2.184322 CGTCCATACGCAGCCAGT 59.816 61.111 0.00 0.00 43.12 4.00
173 174 2.167219 CGTCCATACGCAGCCAGTG 61.167 63.158 0.00 0.00 43.12 3.66
193 194 6.985188 AGTGCGTGACTGATATTATTTTGT 57.015 33.333 0.00 0.00 31.75 2.83
194 195 6.775088 AGTGCGTGACTGATATTATTTTGTG 58.225 36.000 0.00 0.00 31.75 3.33
195 196 6.593770 AGTGCGTGACTGATATTATTTTGTGA 59.406 34.615 0.00 0.00 31.75 3.58
196 197 7.280876 AGTGCGTGACTGATATTATTTTGTGAT 59.719 33.333 0.00 0.00 31.75 3.06
197 198 7.584123 GTGCGTGACTGATATTATTTTGTGATC 59.416 37.037 0.00 0.00 0.00 2.92
198 199 7.495606 TGCGTGACTGATATTATTTTGTGATCT 59.504 33.333 0.00 0.00 0.00 2.75
199 200 8.978539 GCGTGACTGATATTATTTTGTGATCTA 58.021 33.333 0.00 0.00 0.00 1.98
210 211 5.984233 TTTTGTGATCTATGTCCATACGC 57.016 39.130 0.00 0.00 0.00 4.42
211 212 3.282831 TGTGATCTATGTCCATACGCG 57.717 47.619 3.53 3.53 0.00 6.01
212 213 2.030274 TGTGATCTATGTCCATACGCGG 60.030 50.000 12.47 0.00 0.00 6.46
213 214 2.030185 GTGATCTATGTCCATACGCGGT 60.030 50.000 12.47 0.00 0.00 5.68
214 215 2.228103 TGATCTATGTCCATACGCGGTC 59.772 50.000 12.47 0.00 0.00 4.79
215 216 0.589708 TCTATGTCCATACGCGGTCG 59.410 55.000 12.47 0.00 42.43 4.79
225 226 3.759828 CGCGGTCGTTTCGTGGTC 61.760 66.667 0.00 0.00 34.88 4.02
226 227 2.355481 GCGGTCGTTTCGTGGTCT 60.355 61.111 0.00 0.00 0.00 3.85
227 228 2.370393 GCGGTCGTTTCGTGGTCTC 61.370 63.158 0.00 0.00 0.00 3.36
228 229 2.078914 CGGTCGTTTCGTGGTCTCG 61.079 63.158 0.00 0.00 0.00 4.04
229 230 1.731969 GGTCGTTTCGTGGTCTCGG 60.732 63.158 0.00 0.00 0.00 4.63
230 231 1.008079 GTCGTTTCGTGGTCTCGGT 60.008 57.895 0.00 0.00 0.00 4.69
231 232 0.238289 GTCGTTTCGTGGTCTCGGTA 59.762 55.000 0.00 0.00 0.00 4.02
232 233 1.135575 GTCGTTTCGTGGTCTCGGTAT 60.136 52.381 0.00 0.00 0.00 2.73
233 234 2.095853 GTCGTTTCGTGGTCTCGGTATA 59.904 50.000 0.00 0.00 0.00 1.47
234 235 2.945008 TCGTTTCGTGGTCTCGGTATAT 59.055 45.455 0.00 0.00 0.00 0.86
235 236 3.040795 CGTTTCGTGGTCTCGGTATATG 58.959 50.000 0.00 0.00 0.00 1.78
236 237 3.378339 GTTTCGTGGTCTCGGTATATGG 58.622 50.000 0.00 0.00 0.00 2.74
237 238 2.643995 TCGTGGTCTCGGTATATGGA 57.356 50.000 0.00 0.00 0.00 3.41
238 239 3.150458 TCGTGGTCTCGGTATATGGAT 57.850 47.619 0.00 0.00 0.00 3.41
239 240 4.290711 TCGTGGTCTCGGTATATGGATA 57.709 45.455 0.00 0.00 0.00 2.59
240 241 4.851843 TCGTGGTCTCGGTATATGGATAT 58.148 43.478 0.00 0.00 0.00 1.63
241 242 5.993055 TCGTGGTCTCGGTATATGGATATA 58.007 41.667 0.00 0.00 0.00 0.86
242 243 6.417258 TCGTGGTCTCGGTATATGGATATAA 58.583 40.000 0.00 0.00 0.00 0.98
243 244 7.058525 TCGTGGTCTCGGTATATGGATATAAT 58.941 38.462 0.00 0.00 0.00 1.28
244 245 7.558807 TCGTGGTCTCGGTATATGGATATAATT 59.441 37.037 0.00 0.00 0.00 1.40
245 246 8.195436 CGTGGTCTCGGTATATGGATATAATTT 58.805 37.037 0.00 0.00 0.00 1.82
246 247 9.886132 GTGGTCTCGGTATATGGATATAATTTT 57.114 33.333 0.00 0.00 0.00 1.82
275 276 7.981102 ATCTCTAAGGTGGTTTTGTACTTTC 57.019 36.000 0.00 0.00 0.00 2.62
276 277 5.987347 TCTCTAAGGTGGTTTTGTACTTTCG 59.013 40.000 0.00 0.00 0.00 3.46
277 278 5.058490 TCTAAGGTGGTTTTGTACTTTCGG 58.942 41.667 0.00 0.00 0.00 4.30
278 279 3.286329 AGGTGGTTTTGTACTTTCGGT 57.714 42.857 0.00 0.00 0.00 4.69
279 280 2.946990 AGGTGGTTTTGTACTTTCGGTG 59.053 45.455 0.00 0.00 0.00 4.94
280 281 2.944349 GGTGGTTTTGTACTTTCGGTGA 59.056 45.455 0.00 0.00 0.00 4.02
281 282 3.377798 GGTGGTTTTGTACTTTCGGTGAA 59.622 43.478 0.00 0.00 0.00 3.18
282 283 4.345288 GTGGTTTTGTACTTTCGGTGAAC 58.655 43.478 0.00 0.00 0.00 3.18
283 284 4.095334 GTGGTTTTGTACTTTCGGTGAACT 59.905 41.667 0.00 0.00 0.00 3.01
284 285 4.701171 TGGTTTTGTACTTTCGGTGAACTT 59.299 37.500 0.00 0.00 0.00 2.66
285 286 5.183522 TGGTTTTGTACTTTCGGTGAACTTT 59.816 36.000 0.00 0.00 0.00 2.66
286 287 5.513849 GGTTTTGTACTTTCGGTGAACTTTG 59.486 40.000 0.00 0.00 0.00 2.77
287 288 6.316319 GTTTTGTACTTTCGGTGAACTTTGA 58.684 36.000 0.00 0.00 0.00 2.69
288 289 6.687081 TTTGTACTTTCGGTGAACTTTGAT 57.313 33.333 0.00 0.00 0.00 2.57
289 290 7.789273 TTTGTACTTTCGGTGAACTTTGATA 57.211 32.000 0.00 0.00 0.00 2.15
290 291 7.789273 TTGTACTTTCGGTGAACTTTGATAA 57.211 32.000 0.00 0.00 0.00 1.75
291 292 7.972832 TGTACTTTCGGTGAACTTTGATAAT 57.027 32.000 0.00 0.00 0.00 1.28
292 293 9.491675 TTGTACTTTCGGTGAACTTTGATAATA 57.508 29.630 0.00 0.00 0.00 0.98
293 294 9.146984 TGTACTTTCGGTGAACTTTGATAATAG 57.853 33.333 0.00 0.00 0.00 1.73
294 295 9.362539 GTACTTTCGGTGAACTTTGATAATAGA 57.637 33.333 0.00 0.00 0.00 1.98
296 297 9.099454 ACTTTCGGTGAACTTTGATAATAGATC 57.901 33.333 0.00 0.00 0.00 2.75
297 298 9.319143 CTTTCGGTGAACTTTGATAATAGATCT 57.681 33.333 0.00 0.00 0.00 2.75
298 299 8.648557 TTCGGTGAACTTTGATAATAGATCTG 57.351 34.615 5.18 0.00 0.00 2.90
299 300 7.210174 TCGGTGAACTTTGATAATAGATCTGG 58.790 38.462 5.18 0.00 0.00 3.86
300 301 7.069455 TCGGTGAACTTTGATAATAGATCTGGA 59.931 37.037 5.18 0.00 0.00 3.86
301 302 7.875041 CGGTGAACTTTGATAATAGATCTGGAT 59.125 37.037 5.18 0.00 0.00 3.41
302 303 9.213799 GGTGAACTTTGATAATAGATCTGGATC 57.786 37.037 5.18 5.99 38.09 3.36
303 304 9.770097 GTGAACTTTGATAATAGATCTGGATCA 57.230 33.333 5.18 8.52 40.22 2.92
304 305 9.770097 TGAACTTTGATAATAGATCTGGATCAC 57.230 33.333 5.18 0.87 40.22 3.06
305 306 9.995003 GAACTTTGATAATAGATCTGGATCACT 57.005 33.333 5.18 0.00 40.22 3.41
309 310 9.481340 TTTGATAATAGATCTGGATCACTTTCG 57.519 33.333 5.18 0.00 40.22 3.46
310 311 8.183104 TGATAATAGATCTGGATCACTTTCGT 57.817 34.615 5.18 0.00 40.22 3.85
311 312 9.297037 TGATAATAGATCTGGATCACTTTCGTA 57.703 33.333 5.18 0.00 40.22 3.43
366 367 7.692291 GTGTGTAAAATGAGATTTATGGACACG 59.308 37.037 0.00 0.00 36.07 4.49
404 405 4.457257 GGAACATCTTTGAGCTTTGCTACT 59.543 41.667 0.00 0.00 39.88 2.57
405 406 5.643777 GGAACATCTTTGAGCTTTGCTACTA 59.356 40.000 0.00 0.00 39.88 1.82
406 407 6.402658 GGAACATCTTTGAGCTTTGCTACTAC 60.403 42.308 0.00 0.00 39.88 2.73
429 430 1.207390 GCAATGTGCAAAGCGTTTGA 58.793 45.000 12.62 0.00 44.26 2.69
430 431 1.794116 GCAATGTGCAAAGCGTTTGAT 59.206 42.857 12.62 0.00 44.26 2.57
431 432 2.221517 GCAATGTGCAAAGCGTTTGATT 59.778 40.909 12.62 3.64 44.26 2.57
441 442 8.058915 GTGCAAAGCGTTTGATTTTGTAAAATA 58.941 29.630 12.62 0.00 43.26 1.40
469 470 3.459232 TCACTCACAAGTCCAGTGAAG 57.541 47.619 8.41 0.00 44.60 3.02
475 476 5.034852 TCACAAGTCCAGTGAAGAAATGA 57.965 39.130 0.00 0.00 42.57 2.57
479 480 7.388776 TCACAAGTCCAGTGAAGAAATGAATAG 59.611 37.037 0.00 0.00 42.57 1.73
480 481 6.150140 ACAAGTCCAGTGAAGAAATGAATAGC 59.850 38.462 0.00 0.00 0.00 2.97
487 488 5.352569 AGTGAAGAAATGAATAGCAGGTTCG 59.647 40.000 0.00 0.00 32.50 3.95
502 564 3.439129 CAGGTTCGAGGAATTAAACACCC 59.561 47.826 0.00 0.00 0.00 4.61
503 565 2.751259 GGTTCGAGGAATTAAACACCCC 59.249 50.000 0.00 0.00 0.00 4.95
504 566 3.560668 GGTTCGAGGAATTAAACACCCCT 60.561 47.826 0.00 0.00 0.00 4.79
505 567 3.343941 TCGAGGAATTAAACACCCCTG 57.656 47.619 0.00 0.00 0.00 4.45
525 587 7.978925 CCCCTGAGGTATTTGATACTCTTATT 58.021 38.462 0.00 0.00 36.04 1.40
552 617 6.636705 TGGCAATATTATCTGATACCCGTAC 58.363 40.000 0.00 0.00 0.00 3.67
553 618 6.439375 TGGCAATATTATCTGATACCCGTACT 59.561 38.462 0.00 0.00 0.00 2.73
554 619 7.616542 TGGCAATATTATCTGATACCCGTACTA 59.383 37.037 0.00 0.00 0.00 1.82
555 620 7.919621 GGCAATATTATCTGATACCCGTACTAC 59.080 40.741 0.00 0.00 0.00 2.73
584 649 0.107800 CTCATCCACACTGAGCTGGG 60.108 60.000 0.00 0.00 34.24 4.45
589 654 1.375652 CACACTGAGCTGGGCTGAG 60.376 63.158 4.59 4.59 45.01 3.35
594 659 0.673022 CTGAGCTGGGCTGAGTTCAC 60.673 60.000 0.00 0.00 39.88 3.18
607 672 2.884012 TGAGTTCACCGCATTTCACATT 59.116 40.909 0.00 0.00 0.00 2.71
615 697 4.266029 CACCGCATTTCACATTCATAAAGC 59.734 41.667 0.00 0.00 0.00 3.51
632 714 8.278729 TCATAAAGCATCACATACATGAACAA 57.721 30.769 0.00 0.00 30.82 2.83
637 719 4.971830 GCATCACATACATGAACAATTCCG 59.028 41.667 0.00 0.00 30.82 4.30
648 730 4.188462 TGAACAATTCCGGTACTGCATAG 58.812 43.478 0.00 0.00 0.00 2.23
649 731 3.906720 ACAATTCCGGTACTGCATAGT 57.093 42.857 0.00 0.00 40.99 2.12
650 732 3.793559 ACAATTCCGGTACTGCATAGTC 58.206 45.455 0.00 0.00 38.36 2.59
653 737 3.520290 TTCCGGTACTGCATAGTCTTG 57.480 47.619 0.00 0.00 38.36 3.02
689 773 1.590591 TAATAAGTCCAGCCAGCCCA 58.409 50.000 0.00 0.00 0.00 5.36
814 898 2.544069 GGGCGAGAGATCTTTCCTTACG 60.544 54.545 7.63 0.00 0.00 3.18
861 945 3.567585 CCATTGTTTTTCCCCGCAATTTT 59.432 39.130 0.00 0.00 30.17 1.82
862 946 4.320129 CCATTGTTTTTCCCCGCAATTTTC 60.320 41.667 0.00 0.00 30.17 2.29
867 951 1.834188 TTCCCCGCAATTTTCTCTCC 58.166 50.000 0.00 0.00 0.00 3.71
942 1026 2.584391 AACCTCCACTCGGCACTCC 61.584 63.158 0.00 0.00 0.00 3.85
961 1055 3.086600 CCACTCTCCCCTGCCCTC 61.087 72.222 0.00 0.00 0.00 4.30
1062 1156 1.324005 CCACCTCCTCCTCGTCTTCC 61.324 65.000 0.00 0.00 0.00 3.46
1071 1165 1.424635 CTCGTCTTCCTCGTCGTCC 59.575 63.158 0.00 0.00 0.00 4.79
1074 1168 1.801983 GTCTTCCTCGTCGTCCTCC 59.198 63.158 0.00 0.00 0.00 4.30
1080 1174 1.820481 CTCGTCGTCCTCCTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
1182 1276 1.456705 GTCCGAGATCAGGGAGCCT 60.457 63.158 5.10 0.00 31.73 4.58
1711 1868 1.203994 ACATGGCGCTTACTACTTCGT 59.796 47.619 7.64 0.00 0.00 3.85
1718 1875 2.858344 CGCTTACTACTTCGTGATTGGG 59.142 50.000 0.00 0.00 0.00 4.12
1774 1932 9.438228 TCCGTCAATCATCTTACTACTATCTAG 57.562 37.037 0.00 0.00 0.00 2.43
1775 1933 8.670135 CCGTCAATCATCTTACTACTATCTAGG 58.330 40.741 0.00 0.00 0.00 3.02
1776 1934 9.438228 CGTCAATCATCTTACTACTATCTAGGA 57.562 37.037 0.00 0.00 0.00 2.94
1779 1937 9.221933 CAATCATCTTACTACTATCTAGGACGT 57.778 37.037 0.00 0.00 0.00 4.34
1780 1938 9.439500 AATCATCTTACTACTATCTAGGACGTC 57.561 37.037 7.13 7.13 0.00 4.34
1781 1939 7.089538 TCATCTTACTACTATCTAGGACGTCG 58.910 42.308 9.92 0.00 0.00 5.12
1782 1940 5.226396 TCTTACTACTATCTAGGACGTCGC 58.774 45.833 9.92 2.53 0.00 5.19
1851 2009 6.465439 TTCCTTTCTTCTTTTCCAAGTTCC 57.535 37.500 0.00 0.00 0.00 3.62
1876 2035 2.445654 CTCCCTCTGCCTCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
1879 2038 2.445654 CCTCTGCCTCCTCCCCTC 60.446 72.222 0.00 0.00 0.00 4.30
1919 2078 4.097286 TCCTTTACCAAAATTAGGATGCGC 59.903 41.667 0.00 0.00 0.00 6.09
1920 2079 3.684103 TTACCAAAATTAGGATGCGCG 57.316 42.857 0.00 0.00 0.00 6.86
1951 2110 9.211485 TGTATAAAGTTAGTTTCTTTTCCTCCG 57.789 33.333 0.00 0.00 36.65 4.63
1952 2111 5.434352 AAAGTTAGTTTCTTTTCCTCCGC 57.566 39.130 0.00 0.00 32.14 5.54
1953 2112 4.353383 AGTTAGTTTCTTTTCCTCCGCT 57.647 40.909 0.00 0.00 0.00 5.52
1954 2113 4.316645 AGTTAGTTTCTTTTCCTCCGCTC 58.683 43.478 0.00 0.00 0.00 5.03
2017 2176 7.439108 ACAAGCATCTTATCTTACCTTACCT 57.561 36.000 0.00 0.00 0.00 3.08
2099 2259 9.563898 CAAATTGACAGCGATATTTATGCATAT 57.436 29.630 7.36 0.00 0.00 1.78
2103 2263 9.435688 TTGACAGCGATATTTATGCATATTACT 57.564 29.630 7.36 0.00 0.00 2.24
2104 2264 9.435688 TGACAGCGATATTTATGCATATTACTT 57.564 29.630 7.36 0.00 0.00 2.24
2107 2267 9.494479 CAGCGATATTTATGCATATTACTTTGG 57.506 33.333 7.36 0.00 0.00 3.28
2108 2268 8.677300 AGCGATATTTATGCATATTACTTTGGG 58.323 33.333 7.36 0.00 0.00 4.12
2109 2269 8.673711 GCGATATTTATGCATATTACTTTGGGA 58.326 33.333 7.36 0.00 0.00 4.37
2110 2270 9.988350 CGATATTTATGCATATTACTTTGGGAC 57.012 33.333 7.36 0.00 0.00 4.46
2130 2290 1.266989 CTTTTCCCGGACTTGACAAGC 59.733 52.381 15.24 7.93 0.00 4.01
2152 2312 2.029365 GGAGAGCGACGTTTAAGCAATC 59.971 50.000 0.00 0.00 0.00 2.67
2164 2324 6.033966 CGTTTAAGCAATCCCATTTTACTCC 58.966 40.000 0.00 0.00 0.00 3.85
2178 2338 3.812019 CTCCCCGGTCGTCGTCAG 61.812 72.222 0.00 0.00 37.11 3.51
2257 2417 4.514577 CAGGCCTACGAGCACCGG 62.515 72.222 3.98 0.00 43.93 5.28
2273 2433 3.734902 GCACCGGAAACCATTGATTGATC 60.735 47.826 9.46 0.00 0.00 2.92
2275 2435 3.947834 ACCGGAAACCATTGATTGATCTC 59.052 43.478 9.46 0.00 0.00 2.75
2307 2467 3.529341 CTGCAGTGGCGGTGGTACA 62.529 63.158 5.25 0.00 45.35 2.90
2407 2567 0.175073 CTCCCGGGCTACTGTAACAC 59.825 60.000 18.49 0.00 0.00 3.32
2408 2568 0.542467 TCCCGGGCTACTGTAACACA 60.542 55.000 18.49 0.00 0.00 3.72
2411 2571 1.674817 CCGGGCTACTGTAACACAAGG 60.675 57.143 0.00 0.00 0.00 3.61
2413 2573 1.339727 GGGCTACTGTAACACAAGGGG 60.340 57.143 0.00 0.00 0.00 4.79
2415 2575 2.354805 GGCTACTGTAACACAAGGGGAG 60.355 54.545 0.00 0.00 0.00 4.30
2417 2577 3.368531 GCTACTGTAACACAAGGGGAGAG 60.369 52.174 0.00 0.00 0.00 3.20
2579 2751 3.053896 CGAGCCCGTCCAAAACCC 61.054 66.667 0.00 0.00 0.00 4.11
2596 2768 4.052229 CGCACCGGAACCGAGTCT 62.052 66.667 9.46 0.00 42.83 3.24
2597 2769 2.432628 GCACCGGAACCGAGTCTG 60.433 66.667 9.46 5.53 42.83 3.51
2599 2771 3.692406 ACCGGAACCGAGTCTGGC 61.692 66.667 9.46 0.00 46.63 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.204941 GACCACTACCGCTGTCAGAAT 59.795 52.381 3.32 0.00 0.00 2.40
8 9 0.601558 GACCACTACCGCTGTCAGAA 59.398 55.000 3.32 0.00 0.00 3.02
9 10 1.583495 CGACCACTACCGCTGTCAGA 61.583 60.000 3.32 0.00 0.00 3.27
10 11 1.154016 CGACCACTACCGCTGTCAG 60.154 63.158 0.00 0.00 0.00 3.51
11 12 1.457823 AACGACCACTACCGCTGTCA 61.458 55.000 0.00 0.00 0.00 3.58
12 13 0.319297 AAACGACCACTACCGCTGTC 60.319 55.000 0.00 0.00 0.00 3.51
13 14 0.599204 CAAACGACCACTACCGCTGT 60.599 55.000 0.00 0.00 0.00 4.40
14 15 1.289109 CCAAACGACCACTACCGCTG 61.289 60.000 0.00 0.00 0.00 5.18
15 16 1.005394 CCAAACGACCACTACCGCT 60.005 57.895 0.00 0.00 0.00 5.52
16 17 1.301165 ACCAAACGACCACTACCGC 60.301 57.895 0.00 0.00 0.00 5.68
17 18 0.947180 CCACCAAACGACCACTACCG 60.947 60.000 0.00 0.00 0.00 4.02
18 19 0.107268 ACCACCAAACGACCACTACC 59.893 55.000 0.00 0.00 0.00 3.18
19 20 1.069668 AGACCACCAAACGACCACTAC 59.930 52.381 0.00 0.00 0.00 2.73
20 21 1.342174 GAGACCACCAAACGACCACTA 59.658 52.381 0.00 0.00 0.00 2.74
21 22 0.106149 GAGACCACCAAACGACCACT 59.894 55.000 0.00 0.00 0.00 4.00
22 23 0.106149 AGAGACCACCAAACGACCAC 59.894 55.000 0.00 0.00 0.00 4.16
23 24 0.834612 AAGAGACCACCAAACGACCA 59.165 50.000 0.00 0.00 0.00 4.02
24 25 1.963172 AAAGAGACCACCAAACGACC 58.037 50.000 0.00 0.00 0.00 4.79
42 43 5.993748 AATCTTCCTTTATCCCGCAAAAA 57.006 34.783 0.00 0.00 0.00 1.94
43 44 5.478679 TGAAATCTTCCTTTATCCCGCAAAA 59.521 36.000 0.00 0.00 0.00 2.44
44 45 5.013547 TGAAATCTTCCTTTATCCCGCAAA 58.986 37.500 0.00 0.00 0.00 3.68
45 46 4.594970 TGAAATCTTCCTTTATCCCGCAA 58.405 39.130 0.00 0.00 0.00 4.85
46 47 4.229304 TGAAATCTTCCTTTATCCCGCA 57.771 40.909 0.00 0.00 0.00 5.69
47 48 5.299279 TGAATGAAATCTTCCTTTATCCCGC 59.701 40.000 0.00 0.00 0.00 6.13
48 49 6.942532 TGAATGAAATCTTCCTTTATCCCG 57.057 37.500 0.00 0.00 0.00 5.14
49 50 8.917088 TGAATGAATGAAATCTTCCTTTATCCC 58.083 33.333 0.00 0.00 0.00 3.85
52 53 9.793252 CGTTGAATGAATGAAATCTTCCTTTAT 57.207 29.630 0.00 0.00 0.00 1.40
53 54 9.008965 TCGTTGAATGAATGAAATCTTCCTTTA 57.991 29.630 0.00 0.00 0.00 1.85
54 55 7.885297 TCGTTGAATGAATGAAATCTTCCTTT 58.115 30.769 0.00 0.00 0.00 3.11
55 56 7.362401 CCTCGTTGAATGAATGAAATCTTCCTT 60.362 37.037 0.00 0.00 0.00 3.36
56 57 6.094603 CCTCGTTGAATGAATGAAATCTTCCT 59.905 38.462 0.00 0.00 0.00 3.36
57 58 6.261118 CCTCGTTGAATGAATGAAATCTTCC 58.739 40.000 0.00 0.00 0.00 3.46
58 59 5.741040 GCCTCGTTGAATGAATGAAATCTTC 59.259 40.000 0.00 0.00 0.00 2.87
59 60 5.416952 AGCCTCGTTGAATGAATGAAATCTT 59.583 36.000 0.00 0.00 0.00 2.40
60 61 4.946157 AGCCTCGTTGAATGAATGAAATCT 59.054 37.500 0.00 0.00 0.00 2.40
61 62 5.240713 AGCCTCGTTGAATGAATGAAATC 57.759 39.130 0.00 0.00 0.00 2.17
62 63 5.416952 AGAAGCCTCGTTGAATGAATGAAAT 59.583 36.000 0.00 0.00 0.00 2.17
63 64 4.761739 AGAAGCCTCGTTGAATGAATGAAA 59.238 37.500 0.00 0.00 0.00 2.69
64 65 4.326826 AGAAGCCTCGTTGAATGAATGAA 58.673 39.130 0.00 0.00 0.00 2.57
65 66 3.935203 GAGAAGCCTCGTTGAATGAATGA 59.065 43.478 0.00 0.00 0.00 2.57
66 67 4.270178 GAGAAGCCTCGTTGAATGAATG 57.730 45.455 0.00 0.00 0.00 2.67
81 82 0.742635 CCTTTCAGAGGCCGAGAAGC 60.743 60.000 0.00 0.00 39.09 3.86
82 83 3.450028 CCTTTCAGAGGCCGAGAAG 57.550 57.895 0.00 0.00 39.09 2.85
91 92 3.567164 ACTGCATTGTGAACCTTTCAGAG 59.433 43.478 0.00 0.00 41.01 3.35
92 93 3.554934 ACTGCATTGTGAACCTTTCAGA 58.445 40.909 0.00 0.00 41.01 3.27
93 94 3.567164 AGACTGCATTGTGAACCTTTCAG 59.433 43.478 0.00 0.00 41.01 3.02
94 95 3.554934 AGACTGCATTGTGAACCTTTCA 58.445 40.909 0.00 0.00 37.33 2.69
95 96 5.689383 TTAGACTGCATTGTGAACCTTTC 57.311 39.130 0.00 0.00 0.00 2.62
96 97 5.183904 GGATTAGACTGCATTGTGAACCTTT 59.816 40.000 0.00 0.00 0.00 3.11
97 98 4.702131 GGATTAGACTGCATTGTGAACCTT 59.298 41.667 0.00 0.00 0.00 3.50
98 99 4.265073 GGATTAGACTGCATTGTGAACCT 58.735 43.478 0.00 0.00 0.00 3.50
99 100 3.378427 GGGATTAGACTGCATTGTGAACC 59.622 47.826 0.00 0.00 0.00 3.62
100 101 3.063997 CGGGATTAGACTGCATTGTGAAC 59.936 47.826 0.00 0.00 0.00 3.18
101 102 3.055458 TCGGGATTAGACTGCATTGTGAA 60.055 43.478 0.00 0.00 0.00 3.18
102 103 2.499693 TCGGGATTAGACTGCATTGTGA 59.500 45.455 0.00 0.00 0.00 3.58
103 104 2.905075 TCGGGATTAGACTGCATTGTG 58.095 47.619 0.00 0.00 0.00 3.33
104 105 3.733337 GATCGGGATTAGACTGCATTGT 58.267 45.455 0.00 0.00 0.00 2.71
105 106 2.733552 CGATCGGGATTAGACTGCATTG 59.266 50.000 7.38 0.00 0.00 2.82
106 107 2.365617 ACGATCGGGATTAGACTGCATT 59.634 45.455 20.98 0.00 0.00 3.56
107 108 1.964223 ACGATCGGGATTAGACTGCAT 59.036 47.619 20.98 0.00 0.00 3.96
108 109 1.067060 CACGATCGGGATTAGACTGCA 59.933 52.381 20.98 0.00 0.00 4.41
109 110 1.337071 TCACGATCGGGATTAGACTGC 59.663 52.381 17.88 0.00 0.00 4.40
110 111 2.287668 GGTCACGATCGGGATTAGACTG 60.288 54.545 25.01 6.79 0.00 3.51
111 112 1.955080 GGTCACGATCGGGATTAGACT 59.045 52.381 25.01 0.00 0.00 3.24
112 113 1.679680 TGGTCACGATCGGGATTAGAC 59.320 52.381 25.01 16.68 0.00 2.59
113 114 1.679680 GTGGTCACGATCGGGATTAGA 59.320 52.381 25.01 4.90 0.00 2.10
114 115 1.407618 TGTGGTCACGATCGGGATTAG 59.592 52.381 25.01 3.56 0.00 1.73
115 116 1.135527 GTGTGGTCACGATCGGGATTA 59.864 52.381 25.01 12.84 34.79 1.75
116 117 0.108329 GTGTGGTCACGATCGGGATT 60.108 55.000 25.01 0.00 34.79 3.01
117 118 1.254975 TGTGTGGTCACGATCGGGAT 61.255 55.000 25.01 0.00 46.49 3.85
118 119 1.873270 CTGTGTGGTCACGATCGGGA 61.873 60.000 17.88 17.88 46.49 5.14
119 120 1.446099 CTGTGTGGTCACGATCGGG 60.446 63.158 20.98 16.98 46.49 5.14
120 121 2.094659 GCTGTGTGGTCACGATCGG 61.095 63.158 20.98 8.65 46.49 4.18
121 122 2.094659 GGCTGTGTGGTCACGATCG 61.095 63.158 14.88 14.88 46.49 3.69
122 123 2.094659 CGGCTGTGTGGTCACGATC 61.095 63.158 0.00 0.00 46.49 3.69
123 124 2.048222 CGGCTGTGTGGTCACGAT 60.048 61.111 0.00 0.00 46.49 3.73
124 125 3.533105 ACGGCTGTGTGGTCACGA 61.533 61.111 0.00 0.00 46.49 4.35
125 126 3.337889 CACGGCTGTGTGGTCACG 61.338 66.667 17.96 0.00 46.49 4.35
139 140 2.724721 CGTAGTATCCCGCGCACG 60.725 66.667 8.75 2.73 39.67 5.34
140 141 2.410469 ACGTAGTATCCCGCGCAC 59.590 61.111 8.75 0.00 41.94 5.34
156 157 2.464459 GCACTGGCTGCGTATGGAC 61.464 63.158 0.00 0.00 35.72 4.02
157 158 2.125147 GCACTGGCTGCGTATGGA 60.125 61.111 0.00 0.00 35.72 3.41
164 165 3.720193 CAGTCACGCACTGGCTGC 61.720 66.667 7.14 0.00 45.57 5.25
170 171 6.593770 TCACAAAATAATATCAGTCACGCACT 59.406 34.615 0.00 0.00 34.67 4.40
171 172 6.771076 TCACAAAATAATATCAGTCACGCAC 58.229 36.000 0.00 0.00 0.00 5.34
172 173 6.976636 TCACAAAATAATATCAGTCACGCA 57.023 33.333 0.00 0.00 0.00 5.24
173 174 7.855545 AGATCACAAAATAATATCAGTCACGC 58.144 34.615 0.00 0.00 0.00 5.34
184 185 8.721478 GCGTATGGACATAGATCACAAAATAAT 58.279 33.333 0.00 0.00 0.00 1.28
185 186 7.095816 CGCGTATGGACATAGATCACAAAATAA 60.096 37.037 0.00 0.00 0.00 1.40
186 187 6.364976 CGCGTATGGACATAGATCACAAAATA 59.635 38.462 0.00 0.00 0.00 1.40
187 188 5.177511 CGCGTATGGACATAGATCACAAAAT 59.822 40.000 0.00 0.00 0.00 1.82
188 189 4.506288 CGCGTATGGACATAGATCACAAAA 59.494 41.667 0.00 0.00 0.00 2.44
189 190 4.048504 CGCGTATGGACATAGATCACAAA 58.951 43.478 0.00 0.00 0.00 2.83
190 191 3.552068 CCGCGTATGGACATAGATCACAA 60.552 47.826 4.92 0.00 0.00 3.33
191 192 2.030274 CCGCGTATGGACATAGATCACA 60.030 50.000 4.92 0.00 0.00 3.58
192 193 2.030185 ACCGCGTATGGACATAGATCAC 60.030 50.000 4.92 0.00 0.00 3.06
193 194 2.228103 GACCGCGTATGGACATAGATCA 59.772 50.000 4.92 0.00 0.00 2.92
194 195 2.728225 CGACCGCGTATGGACATAGATC 60.728 54.545 4.92 0.00 0.00 2.75
195 196 1.199327 CGACCGCGTATGGACATAGAT 59.801 52.381 4.92 0.00 0.00 1.98
196 197 0.589708 CGACCGCGTATGGACATAGA 59.410 55.000 4.92 0.00 0.00 1.98
197 198 3.087638 CGACCGCGTATGGACATAG 57.912 57.895 4.92 0.00 0.00 2.23
208 209 3.759828 GACCACGAAACGACCGCG 61.760 66.667 0.00 0.00 44.79 6.46
209 210 2.355481 AGACCACGAAACGACCGC 60.355 61.111 0.00 0.00 0.00 5.68
210 211 2.078914 CGAGACCACGAAACGACCG 61.079 63.158 0.00 0.00 35.09 4.79
211 212 1.731969 CCGAGACCACGAAACGACC 60.732 63.158 0.00 0.00 35.09 4.79
212 213 0.238289 TACCGAGACCACGAAACGAC 59.762 55.000 0.00 0.00 35.09 4.34
213 214 1.167851 ATACCGAGACCACGAAACGA 58.832 50.000 0.00 0.00 35.09 3.85
214 215 2.830772 TATACCGAGACCACGAAACG 57.169 50.000 0.00 0.00 35.09 3.60
215 216 3.067180 TCCATATACCGAGACCACGAAAC 59.933 47.826 0.00 0.00 35.09 2.78
216 217 3.289836 TCCATATACCGAGACCACGAAA 58.710 45.455 0.00 0.00 35.09 3.46
217 218 2.934887 TCCATATACCGAGACCACGAA 58.065 47.619 0.00 0.00 35.09 3.85
218 219 2.643995 TCCATATACCGAGACCACGA 57.356 50.000 0.00 0.00 35.09 4.35
219 220 6.688637 TTATATCCATATACCGAGACCACG 57.311 41.667 0.00 0.00 0.00 4.94
220 221 9.886132 AAAATTATATCCATATACCGAGACCAC 57.114 33.333 0.00 0.00 0.00 4.16
249 250 9.498176 GAAAGTACAAAACCACCTTAGAGATAA 57.502 33.333 0.00 0.00 0.00 1.75
250 251 7.816031 CGAAAGTACAAAACCACCTTAGAGATA 59.184 37.037 0.00 0.00 0.00 1.98
251 252 6.649557 CGAAAGTACAAAACCACCTTAGAGAT 59.350 38.462 0.00 0.00 0.00 2.75
252 253 5.987347 CGAAAGTACAAAACCACCTTAGAGA 59.013 40.000 0.00 0.00 0.00 3.10
253 254 5.178809 CCGAAAGTACAAAACCACCTTAGAG 59.821 44.000 0.00 0.00 0.00 2.43
254 255 5.058490 CCGAAAGTACAAAACCACCTTAGA 58.942 41.667 0.00 0.00 0.00 2.10
255 256 4.818005 ACCGAAAGTACAAAACCACCTTAG 59.182 41.667 0.00 0.00 0.00 2.18
256 257 4.575645 CACCGAAAGTACAAAACCACCTTA 59.424 41.667 0.00 0.00 0.00 2.69
257 258 3.379057 CACCGAAAGTACAAAACCACCTT 59.621 43.478 0.00 0.00 0.00 3.50
258 259 2.946990 CACCGAAAGTACAAAACCACCT 59.053 45.455 0.00 0.00 0.00 4.00
259 260 2.944349 TCACCGAAAGTACAAAACCACC 59.056 45.455 0.00 0.00 0.00 4.61
260 261 4.095334 AGTTCACCGAAAGTACAAAACCAC 59.905 41.667 0.00 0.00 0.00 4.16
261 262 4.263435 AGTTCACCGAAAGTACAAAACCA 58.737 39.130 0.00 0.00 0.00 3.67
262 263 4.888038 AGTTCACCGAAAGTACAAAACC 57.112 40.909 0.00 0.00 0.00 3.27
263 264 6.316319 TCAAAGTTCACCGAAAGTACAAAAC 58.684 36.000 0.00 0.00 0.00 2.43
264 265 6.497785 TCAAAGTTCACCGAAAGTACAAAA 57.502 33.333 0.00 0.00 0.00 2.44
265 266 6.687081 ATCAAAGTTCACCGAAAGTACAAA 57.313 33.333 0.00 0.00 0.00 2.83
266 267 7.789273 TTATCAAAGTTCACCGAAAGTACAA 57.211 32.000 0.00 0.00 0.00 2.41
267 268 7.972832 ATTATCAAAGTTCACCGAAAGTACA 57.027 32.000 0.00 0.00 0.00 2.90
268 269 9.362539 TCTATTATCAAAGTTCACCGAAAGTAC 57.637 33.333 0.00 0.00 0.00 2.73
270 271 9.099454 GATCTATTATCAAAGTTCACCGAAAGT 57.901 33.333 0.00 0.00 0.00 2.66
271 272 9.319143 AGATCTATTATCAAAGTTCACCGAAAG 57.681 33.333 0.00 0.00 0.00 2.62
272 273 9.098355 CAGATCTATTATCAAAGTTCACCGAAA 57.902 33.333 0.00 0.00 0.00 3.46
273 274 7.710907 CCAGATCTATTATCAAAGTTCACCGAA 59.289 37.037 0.00 0.00 0.00 4.30
274 275 7.069455 TCCAGATCTATTATCAAAGTTCACCGA 59.931 37.037 0.00 0.00 0.00 4.69
275 276 7.210174 TCCAGATCTATTATCAAAGTTCACCG 58.790 38.462 0.00 0.00 0.00 4.94
276 277 9.213799 GATCCAGATCTATTATCAAAGTTCACC 57.786 37.037 0.00 0.00 35.04 4.02
277 278 9.770097 TGATCCAGATCTATTATCAAAGTTCAC 57.230 33.333 8.99 0.00 38.60 3.18
278 279 9.770097 GTGATCCAGATCTATTATCAAAGTTCA 57.230 33.333 12.79 0.00 38.60 3.18
279 280 9.995003 AGTGATCCAGATCTATTATCAAAGTTC 57.005 33.333 12.79 4.17 38.60 3.01
283 284 9.481340 CGAAAGTGATCCAGATCTATTATCAAA 57.519 33.333 12.79 0.00 38.60 2.69
284 285 8.642432 ACGAAAGTGATCCAGATCTATTATCAA 58.358 33.333 12.79 0.20 46.97 2.57
285 286 8.183104 ACGAAAGTGATCCAGATCTATTATCA 57.817 34.615 8.99 2.35 46.97 2.15
338 339 9.295825 TGTCCATAAATCTCATTTTACACACTT 57.704 29.630 0.00 0.00 33.82 3.16
342 343 7.148306 ACCGTGTCCATAAATCTCATTTTACAC 60.148 37.037 0.00 0.00 33.82 2.90
441 442 5.418840 ACTGGACTTGTGAGTGAAATGTTTT 59.581 36.000 0.00 0.00 35.88 2.43
469 470 4.442706 TCCTCGAACCTGCTATTCATTTC 58.557 43.478 0.00 0.00 0.00 2.17
475 476 6.093633 GTGTTTAATTCCTCGAACCTGCTATT 59.906 38.462 0.00 0.00 0.00 1.73
479 480 3.119955 GGTGTTTAATTCCTCGAACCTGC 60.120 47.826 0.00 0.00 0.00 4.85
480 481 3.439129 GGGTGTTTAATTCCTCGAACCTG 59.561 47.826 0.00 0.00 0.00 4.00
487 488 3.621558 CCTCAGGGGTGTTTAATTCCTC 58.378 50.000 0.00 0.00 0.00 3.71
505 567 9.952188 GCCAAAAATAAGAGTATCAAATACCTC 57.048 33.333 0.00 0.00 37.82 3.85
525 587 7.001674 ACGGGTATCAGATAATATTGCCAAAA 58.998 34.615 0.00 0.00 0.00 2.44
536 601 8.377799 TCATGTAGTAGTACGGGTATCAGATAA 58.622 37.037 3.32 0.00 30.95 1.75
540 605 6.872628 TTCATGTAGTAGTACGGGTATCAG 57.127 41.667 3.32 0.00 30.95 2.90
552 617 6.922407 CAGTGTGGATGAGATTCATGTAGTAG 59.078 42.308 0.00 0.00 37.20 2.57
553 618 6.607198 TCAGTGTGGATGAGATTCATGTAGTA 59.393 38.462 0.00 0.00 37.20 1.82
554 619 5.423290 TCAGTGTGGATGAGATTCATGTAGT 59.577 40.000 0.00 0.00 37.20 2.73
555 620 5.910614 TCAGTGTGGATGAGATTCATGTAG 58.089 41.667 0.00 0.00 37.20 2.74
584 649 0.874390 TGAAATGCGGTGAACTCAGC 59.126 50.000 0.00 0.00 40.68 4.26
589 654 3.281341 TGAATGTGAAATGCGGTGAAC 57.719 42.857 0.00 0.00 0.00 3.18
590 655 5.635417 TTATGAATGTGAAATGCGGTGAA 57.365 34.783 0.00 0.00 0.00 3.18
594 659 4.422840 TGCTTTATGAATGTGAAATGCGG 58.577 39.130 0.00 0.00 0.00 5.69
607 672 7.862512 TGTTCATGTATGTGATGCTTTATGA 57.137 32.000 0.00 0.00 0.00 2.15
615 697 5.066375 ACCGGAATTGTTCATGTATGTGATG 59.934 40.000 9.46 0.00 0.00 3.07
632 714 3.704566 TCAAGACTATGCAGTACCGGAAT 59.295 43.478 9.46 0.00 34.21 3.01
637 719 3.733337 CCCATCAAGACTATGCAGTACC 58.267 50.000 0.00 0.00 34.21 3.34
648 730 1.906105 TACACCCGGCCCATCAAGAC 61.906 60.000 0.00 0.00 0.00 3.01
649 731 1.202099 TTACACCCGGCCCATCAAGA 61.202 55.000 0.00 0.00 0.00 3.02
650 732 0.322997 TTTACACCCGGCCCATCAAG 60.323 55.000 0.00 0.00 0.00 3.02
653 737 2.351706 TTATTTACACCCGGCCCATC 57.648 50.000 0.00 0.00 0.00 3.51
699 783 1.635844 CGTTCATTGAACCGGATCGA 58.364 50.000 20.87 6.19 39.14 3.59
700 784 0.026285 GCGTTCATTGAACCGGATCG 59.974 55.000 20.87 11.14 39.14 3.69
814 898 2.738314 GTGCTGAAATTTGAACCCATGC 59.262 45.455 0.00 0.00 0.00 4.06
942 1026 3.721706 GGGCAGGGGAGAGTGGTG 61.722 72.222 0.00 0.00 0.00 4.17
961 1055 0.470268 GAGGAGTAGGTAGGCAGGGG 60.470 65.000 0.00 0.00 0.00 4.79
1038 1132 3.462678 GAGGAGGAGGTGGCCGTC 61.463 72.222 0.00 0.00 0.00 4.79
1062 1156 1.820481 GGAGGAGGAGGACGACGAG 60.820 68.421 0.00 0.00 0.00 4.18
1484 1619 3.703127 GGGCGTCTTCCGGGTCTT 61.703 66.667 0.00 0.00 36.94 3.01
1485 1620 4.698625 AGGGCGTCTTCCGGGTCT 62.699 66.667 0.00 0.00 36.94 3.85
1491 1626 1.737008 GTCGAACAGGGCGTCTTCC 60.737 63.158 0.00 0.00 0.00 3.46
1698 1855 2.608090 GCCCAATCACGAAGTAGTAAGC 59.392 50.000 0.00 0.00 41.61 3.09
1711 1868 1.760480 TCTCCGATCGGCCCAATCA 60.760 57.895 29.62 9.34 34.68 2.57
1718 1875 0.179084 TTTCCATGTCTCCGATCGGC 60.179 55.000 29.62 15.99 34.68 5.54
1782 1940 2.484203 GGAGGAAGACGACGACGG 59.516 66.667 12.58 0.00 44.46 4.79
1818 1976 4.292977 AGAAGAAAGGAAAAACACAGCG 57.707 40.909 0.00 0.00 0.00 5.18
1859 2018 2.445654 GGGAGGAGGCAGAGGGAG 60.446 72.222 0.00 0.00 0.00 4.30
1876 2035 2.681152 AAAGTAAAAACGCAGCGAGG 57.319 45.000 24.65 0.00 0.00 4.63
1879 2038 2.994849 AGGAAAAGTAAAAACGCAGCG 58.005 42.857 14.82 14.82 0.00 5.18
1951 2110 0.457337 CCAAATCAAGCAAGGCGAGC 60.457 55.000 0.00 0.00 0.00 5.03
1952 2111 0.171903 CCCAAATCAAGCAAGGCGAG 59.828 55.000 0.00 0.00 0.00 5.03
1953 2112 1.250154 CCCCAAATCAAGCAAGGCGA 61.250 55.000 0.00 0.00 0.00 5.54
1954 2113 1.216178 CCCCAAATCAAGCAAGGCG 59.784 57.895 0.00 0.00 0.00 5.52
2025 2184 9.511144 CCTTTTACCGCTAAACAAATAAATAGG 57.489 33.333 0.00 0.00 0.00 2.57
2026 2185 9.511144 CCCTTTTACCGCTAAACAAATAAATAG 57.489 33.333 0.00 0.00 0.00 1.73
2032 2191 3.366577 CGCCCTTTTACCGCTAAACAAAT 60.367 43.478 0.00 0.00 0.00 2.32
2107 2267 1.202722 TGTCAAGTCCGGGAAAAGTCC 60.203 52.381 0.00 0.00 44.10 3.85
2108 2268 2.249844 TGTCAAGTCCGGGAAAAGTC 57.750 50.000 0.00 0.00 0.00 3.01
2109 2269 2.572290 CTTGTCAAGTCCGGGAAAAGT 58.428 47.619 0.00 0.00 0.00 2.66
2110 2270 1.266989 GCTTGTCAAGTCCGGGAAAAG 59.733 52.381 14.03 2.54 32.59 2.27
2111 2271 1.314730 GCTTGTCAAGTCCGGGAAAA 58.685 50.000 14.03 0.00 0.00 2.29
2115 2275 2.742372 CCGCTTGTCAAGTCCGGG 60.742 66.667 18.70 10.30 32.60 5.73
2118 2278 1.016653 GCTCTCCGCTTGTCAAGTCC 61.017 60.000 14.03 0.00 35.14 3.85
2130 2290 0.731514 TGCTTAAACGTCGCTCTCCG 60.732 55.000 0.00 0.00 38.61 4.63
2141 2301 6.338146 GGGAGTAAAATGGGATTGCTTAAAC 58.662 40.000 0.00 0.00 0.00 2.01
2152 2312 0.463116 CGACCGGGGAGTAAAATGGG 60.463 60.000 6.32 0.00 0.00 4.00
2164 2324 4.778415 CTGCTGACGACGACCGGG 62.778 72.222 6.32 0.00 43.93 5.73
2197 2357 1.260206 CTTGACGACGACGAATCCTG 58.740 55.000 15.32 0.00 42.66 3.86
2257 2417 4.889832 AGCGAGATCAATCAATGGTTTC 57.110 40.909 0.00 0.00 0.00 2.78
2307 2467 1.550524 TCAAGCCATTGTAGACTCGCT 59.449 47.619 0.00 0.00 37.68 4.93
2388 2548 0.175073 GTGTTACAGTAGCCCGGGAG 59.825 60.000 29.31 10.36 0.00 4.30
2396 2556 4.087182 TCTCTCCCCTTGTGTTACAGTAG 58.913 47.826 0.00 0.00 0.00 2.57
2425 2585 2.043980 CGGGCGGGCATTAACAACT 61.044 57.895 3.27 0.00 0.00 3.16
2426 2586 2.487892 CGGGCGGGCATTAACAAC 59.512 61.111 3.27 0.00 0.00 3.32
2428 2588 3.980442 GACCGGGCGGGCATTAACA 62.980 63.158 11.50 0.00 44.50 2.41
2429 2589 3.206957 GACCGGGCGGGCATTAAC 61.207 66.667 11.50 0.00 44.50 2.01
2450 2610 4.671590 GGGGTCGTGGGGGTTTGG 62.672 72.222 0.00 0.00 0.00 3.28
2529 2701 4.821589 CGCTGCCCTCGAGGTTCC 62.822 72.222 29.25 17.27 38.26 3.62
2548 2720 4.764336 CTCGTACGTGCGCGGGAA 62.764 66.667 25.20 6.04 43.45 3.97
2579 2751 4.052229 AGACTCGGTTCCGGTGCG 62.052 66.667 11.37 1.21 0.00 5.34


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

AutoCloner maintained by Alex Coulton.