Multiple sequence alignment - TraesCS4B01G148300

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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 TraesCS4B01G148300 chr4B 100.000 3051 0 0 610 3660 213963826 213966876 0.000000e+00 5635.0
1 TraesCS4B01G148300 chr4B 100.000 333 0 0 1 333 213963217 213963549 1.870000e-172 616.0
2 TraesCS4B01G148300 chr4B 90.625 64 5 1 610 672 97314249 97314312 2.340000e-12 84.2
3 TraesCS4B01G148300 chr4B 94.286 35 2 0 299 333 203233596 203233630 2.000000e-03 54.7
4 TraesCS4B01G148300 chr7D 91.762 1918 148 10 1747 3660 72785148 72787059 0.000000e+00 2658.0
5 TraesCS4B01G148300 chr5D 91.795 1426 110 6 2238 3660 489744315 489742894 0.000000e+00 1978.0
6 TraesCS4B01G148300 chr5D 89.189 222 22 1 1514 1733 532474845 532474624 3.600000e-70 276.0
7 TraesCS4B01G148300 chr5D 94.215 121 7 0 1573 1693 489744875 489744755 6.240000e-43 185.0
8 TraesCS4B01G148300 chr6D 90.669 1479 131 7 2185 3660 219292397 219290923 0.000000e+00 1960.0
9 TraesCS4B01G148300 chr6D 88.525 1586 145 23 610 2187 219293916 219292360 0.000000e+00 1886.0
10 TraesCS4B01G148300 chr2D 90.533 1426 113 11 2238 3660 232179607 232178201 0.000000e+00 1866.0
11 TraesCS4B01G148300 chr2D 93.439 442 27 2 1744 2183 232180048 232179607 0.000000e+00 654.0
12 TraesCS4B01G148300 chr2D 96.875 32 1 0 302 333 545483297 545483328 2.000000e-03 54.7
13 TraesCS4B01G148300 chr4D 90.182 1426 130 9 2238 3660 200714917 200713499 0.000000e+00 1849.0
14 TraesCS4B01G148300 chr4D 93.213 442 27 3 1744 2183 200715357 200714917 0.000000e+00 647.0
15 TraesCS4B01G148300 chr2A 89.895 1425 139 5 2238 3660 460472824 460471403 0.000000e+00 1829.0
16 TraesCS4B01G148300 chr2A 89.541 1415 140 7 2249 3660 299510056 299508647 0.000000e+00 1786.0
17 TraesCS4B01G148300 chr2A 92.534 442 30 3 1745 2184 299510506 299510066 6.670000e-177 630.0
18 TraesCS4B01G148300 chr2A 91.270 126 11 0 1573 1698 460473386 460473261 4.860000e-39 172.0
19 TraesCS4B01G148300 chr2A 96.875 32 1 0 302 333 79735139 79735108 2.000000e-03 54.7
20 TraesCS4B01G148300 chr2A 96.875 32 1 0 302 333 687524967 687524936 2.000000e-03 54.7
21 TraesCS4B01G148300 chr3D 90.957 1316 112 6 2348 3660 172531322 172530011 0.000000e+00 1764.0
22 TraesCS4B01G148300 chr3D 92.360 445 31 2 1747 2188 71520939 71520495 6.670000e-177 630.0
23 TraesCS4B01G148300 chr3D 90.076 131 12 1 1573 1702 497288705 497288835 6.290000e-38 169.0
24 TraesCS4B01G148300 chr3D 96.875 32 1 0 302 333 551526417 551526448 2.000000e-03 54.7
25 TraesCS4B01G148300 chr7B 88.850 1426 146 10 2238 3660 193201432 193202847 0.000000e+00 1740.0
26 TraesCS4B01G148300 chr7B 93.213 442 28 2 1744 2183 193200991 193201432 0.000000e+00 649.0
27 TraesCS4B01G148300 chr7B 93.333 165 9 2 2185 2348 310751859 310752022 3.650000e-60 243.0
28 TraesCS4B01G148300 chr7B 90.071 141 13 1 1350 1489 744237116 744237256 8.070000e-42 182.0
29 TraesCS4B01G148300 chr7B 87.500 144 17 1 1350 1492 17502168 17502025 8.130000e-37 165.0
30 TraesCS4B01G148300 chr7B 85.926 135 18 1 1350 1483 743706560 743706694 3.810000e-30 143.0
31 TraesCS4B01G148300 chr7B 84.946 93 12 2 1218 1310 42193844 42193934 3.890000e-15 93.5
32 TraesCS4B01G148300 chr7B 93.220 59 3 1 610 667 638233620 638233678 6.510000e-13 86.1
33 TraesCS4B01G148300 chr7A 92.374 577 42 2 1613 2187 540916234 540916810 0.000000e+00 821.0
34 TraesCS4B01G148300 chr7A 82.483 862 135 10 610 1469 51995925 51996772 0.000000e+00 741.0
35 TraesCS4B01G148300 chr3A 92.360 445 31 2 1747 2188 83751346 83750902 6.670000e-177 630.0
36 TraesCS4B01G148300 chr3A 93.667 300 18 1 4 302 219342773 219342474 7.210000e-122 448.0
37 TraesCS4B01G148300 chr3A 93.667 300 18 1 4 302 334784794 334784495 7.210000e-122 448.0
38 TraesCS4B01G148300 chr3A 100.000 30 0 0 302 331 54533138 54533109 5.110000e-04 56.5
39 TraesCS4B01G148300 chr4A 93.399 303 19 1 1 302 403171917 403172219 7.210000e-122 448.0
40 TraesCS4B01G148300 chr4A 93.289 298 19 1 5 301 304782266 304782563 4.340000e-119 438.0
41 TraesCS4B01G148300 chr4A 87.500 240 24 6 1505 1740 690440570 690440333 4.660000e-69 272.0
42 TraesCS4B01G148300 chr4A 86.301 146 19 1 610 754 723918685 723918540 1.360000e-34 158.0
43 TraesCS4B01G148300 chr2B 93.377 302 19 1 1 301 702728156 702728457 2.590000e-121 446.0
44 TraesCS4B01G148300 chr6A 93.046 302 18 3 1 301 580321923 580322222 4.340000e-119 438.0
45 TraesCS4B01G148300 chr6A 92.982 57 4 0 610 666 265619061 265619005 2.340000e-12 84.2
46 TraesCS4B01G148300 chr1A 92.715 302 18 4 4 302 492810260 492809960 2.020000e-117 433.0
47 TraesCS4B01G148300 chr1A 92.667 300 20 2 4 301 472948705 472948406 7.260000e-117 431.0
48 TraesCS4B01G148300 chr1A 94.643 56 3 0 610 665 18828505 18828450 1.810000e-13 87.9
49 TraesCS4B01G148300 chr1A 94.643 56 3 0 610 665 19005778 19005723 1.810000e-13 87.9
50 TraesCS4B01G148300 chr1A 93.103 58 4 0 610 667 561069809 561069752 6.510000e-13 86.1
51 TraesCS4B01G148300 chr1A 92.982 57 3 1 610 665 587485778 587485834 8.420000e-12 82.4
52 TraesCS4B01G148300 chr3B 90.402 323 25 5 1 320 99121083 99121402 1.570000e-113 420.0
53 TraesCS4B01G148300 chr3B 96.875 32 1 0 302 333 706503989 706503958 2.000000e-03 54.7
54 TraesCS4B01G148300 chr5B 88.412 233 22 5 1505 1734 604449519 604449749 3.600000e-70 276.0
55 TraesCS4B01G148300 chr6B 81.271 299 36 16 3336 3633 142000875 142000596 1.320000e-54 224.0
56 TraesCS4B01G148300 chr6B 94.286 35 2 0 299 333 1653966 1654000 2.000000e-03 54.7
57 TraesCS4B01G148300 chr1B 89.222 167 12 6 1578 1740 501627203 501627039 1.720000e-48 204.0
58 TraesCS4B01G148300 chr5A 87.395 119 14 1 1308 1426 13489946 13489829 6.380000e-28 135.0
59 TraesCS4B01G148300 chr5A 86.517 89 11 1 1218 1306 14578157 14578244 3.010000e-16 97.1
60 TraesCS4B01G148300 chr5A 94.643 56 3 0 610 665 633518963 633519018 1.810000e-13 87.9


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 TraesCS4B01G148300 chr4B 213963217 213966876 3659 False 3125.5 5635 100.0000 1 3660 2 chr4B.!!$F3 3659
1 TraesCS4B01G148300 chr7D 72785148 72787059 1911 False 2658.0 2658 91.7620 1747 3660 1 chr7D.!!$F1 1913
2 TraesCS4B01G148300 chr5D 489742894 489744875 1981 True 1081.5 1978 93.0050 1573 3660 2 chr5D.!!$R2 2087
3 TraesCS4B01G148300 chr6D 219290923 219293916 2993 True 1923.0 1960 89.5970 610 3660 2 chr6D.!!$R1 3050
4 TraesCS4B01G148300 chr2D 232178201 232180048 1847 True 1260.0 1866 91.9860 1744 3660 2 chr2D.!!$R1 1916
5 TraesCS4B01G148300 chr4D 200713499 200715357 1858 True 1248.0 1849 91.6975 1744 3660 2 chr4D.!!$R1 1916
6 TraesCS4B01G148300 chr2A 299508647 299510506 1859 True 1208.0 1786 91.0375 1745 3660 2 chr2A.!!$R3 1915
7 TraesCS4B01G148300 chr2A 460471403 460473386 1983 True 1000.5 1829 90.5825 1573 3660 2 chr2A.!!$R4 2087
8 TraesCS4B01G148300 chr3D 172530011 172531322 1311 True 1764.0 1764 90.9570 2348 3660 1 chr3D.!!$R2 1312
9 TraesCS4B01G148300 chr7B 193200991 193202847 1856 False 1194.5 1740 91.0315 1744 3660 2 chr7B.!!$F6 1916
10 TraesCS4B01G148300 chr7A 540916234 540916810 576 False 821.0 821 92.3740 1613 2187 1 chr7A.!!$F2 574
11 TraesCS4B01G148300 chr7A 51995925 51996772 847 False 741.0 741 82.4830 610 1469 1 chr7A.!!$F1 859

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
327 328 0.188834 CCCAACCACCCAAACCCTAA 59.811 55.0 0.0 0.0 0.00 2.69 F
1062 1071 0.247460 TGATGCTTGACCTCGTCAGG 59.753 55.0 0.0 0.0 43.69 3.86 F
1361 1371 0.106519 AACTTGCAGTCAGGTTGCCT 60.107 50.0 0.0 0.0 40.42 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1358 0.250640 AGAGCAAGGCAACCTGACTG 60.251 55.0 0.0 0.0 31.94 3.51 R
2381 2396 0.036952 CACCTCCTGCACGTCTGATT 60.037 55.0 0.0 0.0 0.00 2.57 R
2841 2857 0.321671 AGACTGAATCCCCACACACG 59.678 55.0 0.0 0.0 0.00 4.49 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
86 87 4.465632 CCCAATAGGCCTAAAAACCAAC 57.534 45.455 18.42 0.00 0.00 3.77
87 88 3.196901 CCCAATAGGCCTAAAAACCAACC 59.803 47.826 18.42 0.00 0.00 3.77
88 89 4.093743 CCAATAGGCCTAAAAACCAACCT 58.906 43.478 18.42 0.00 0.00 3.50
89 90 5.265989 CCAATAGGCCTAAAAACCAACCTA 58.734 41.667 18.42 0.00 34.45 3.08
90 91 5.359860 CCAATAGGCCTAAAAACCAACCTAG 59.640 44.000 18.42 0.00 33.50 3.02
91 92 2.803956 AGGCCTAAAAACCAACCTAGC 58.196 47.619 1.29 0.00 0.00 3.42
92 93 2.109304 AGGCCTAAAAACCAACCTAGCA 59.891 45.455 1.29 0.00 0.00 3.49
93 94 2.492088 GGCCTAAAAACCAACCTAGCAG 59.508 50.000 0.00 0.00 0.00 4.24
94 95 2.492088 GCCTAAAAACCAACCTAGCAGG 59.508 50.000 1.16 1.16 42.49 4.85
95 96 2.492088 CCTAAAAACCAACCTAGCAGGC 59.508 50.000 2.50 0.00 39.63 4.85
96 97 2.381752 AAAAACCAACCTAGCAGGCT 57.618 45.000 0.00 0.00 39.63 4.58
97 98 1.620822 AAAACCAACCTAGCAGGCTG 58.379 50.000 10.94 10.94 39.63 4.85
98 99 0.771127 AAACCAACCTAGCAGGCTGA 59.229 50.000 20.86 0.00 39.63 4.26
99 100 0.771127 AACCAACCTAGCAGGCTGAA 59.229 50.000 20.86 4.05 39.63 3.02
100 101 0.771127 ACCAACCTAGCAGGCTGAAA 59.229 50.000 20.86 3.64 39.63 2.69
101 102 1.144913 ACCAACCTAGCAGGCTGAAAA 59.855 47.619 20.86 0.80 39.63 2.29
102 103 2.225117 ACCAACCTAGCAGGCTGAAAAT 60.225 45.455 20.86 2.82 39.63 1.82
103 104 2.165030 CCAACCTAGCAGGCTGAAAATG 59.835 50.000 20.86 8.43 39.63 2.32
104 105 2.821969 CAACCTAGCAGGCTGAAAATGT 59.178 45.455 20.86 4.98 39.63 2.71
105 106 2.440409 ACCTAGCAGGCTGAAAATGTG 58.560 47.619 20.86 1.50 39.63 3.21
106 107 1.133790 CCTAGCAGGCTGAAAATGTGC 59.866 52.381 20.86 0.00 0.00 4.57
107 108 1.814394 CTAGCAGGCTGAAAATGTGCA 59.186 47.619 20.86 0.00 36.57 4.57
108 109 0.601558 AGCAGGCTGAAAATGTGCAG 59.398 50.000 20.86 0.00 36.57 4.41
113 114 3.806591 CTGAAAATGTGCAGCCCAG 57.193 52.632 0.00 0.00 0.00 4.45
114 115 0.389426 CTGAAAATGTGCAGCCCAGC 60.389 55.000 0.00 0.00 0.00 4.85
115 116 1.444895 GAAAATGTGCAGCCCAGCG 60.445 57.895 0.00 0.00 37.31 5.18
116 117 2.146073 GAAAATGTGCAGCCCAGCGT 62.146 55.000 0.00 0.00 37.31 5.07
117 118 2.424705 AAAATGTGCAGCCCAGCGTG 62.425 55.000 0.00 0.00 37.31 5.34
121 122 4.328025 TGCAGCCCAGCGTGCTAA 62.328 61.111 0.00 0.00 40.54 3.09
122 123 3.055719 GCAGCCCAGCGTGCTAAA 61.056 61.111 0.00 0.00 36.81 1.85
123 124 2.870372 CAGCCCAGCGTGCTAAAC 59.130 61.111 0.00 0.00 36.81 2.01
132 133 3.098555 GTGCTAAACGGGCCATCG 58.901 61.111 4.39 1.48 0.00 3.84
133 134 2.124901 TGCTAAACGGGCCATCGG 60.125 61.111 4.39 0.00 0.00 4.18
134 135 2.900337 GCTAAACGGGCCATCGGG 60.900 66.667 4.39 0.00 37.18 5.14
150 151 2.268600 GGCCGGCCCGTTTACTAA 59.731 61.111 36.64 0.00 0.00 2.24
151 152 1.153107 GGCCGGCCCGTTTACTAAT 60.153 57.895 36.64 0.00 0.00 1.73
152 153 1.162181 GGCCGGCCCGTTTACTAATC 61.162 60.000 36.64 4.14 0.00 1.75
153 154 0.462403 GCCGGCCCGTTTACTAATCA 60.462 55.000 18.11 0.00 0.00 2.57
154 155 1.578583 CCGGCCCGTTTACTAATCAG 58.421 55.000 0.85 0.00 0.00 2.90
155 156 1.578583 CGGCCCGTTTACTAATCAGG 58.421 55.000 0.00 0.00 0.00 3.86
156 157 1.306148 GGCCCGTTTACTAATCAGGC 58.694 55.000 0.00 0.00 38.21 4.85
157 158 1.306148 GCCCGTTTACTAATCAGGCC 58.694 55.000 0.00 0.00 32.68 5.19
158 159 1.578583 CCCGTTTACTAATCAGGCCG 58.421 55.000 0.00 0.00 0.00 6.13
159 160 1.134610 CCCGTTTACTAATCAGGCCGT 60.135 52.381 0.00 0.00 0.00 5.68
160 161 1.931172 CCGTTTACTAATCAGGCCGTG 59.069 52.381 0.00 0.00 0.00 4.94
161 162 1.326548 CGTTTACTAATCAGGCCGTGC 59.673 52.381 0.00 0.00 0.00 5.34
179 180 4.355720 CTGGGCCAAGGAGCAGCA 62.356 66.667 8.04 0.00 0.00 4.41
180 181 4.666253 TGGGCCAAGGAGCAGCAC 62.666 66.667 2.13 0.00 0.00 4.40
184 185 4.335647 CCAAGGAGCAGCACCCGT 62.336 66.667 5.06 0.00 0.00 5.28
185 186 3.052082 CAAGGAGCAGCACCCGTG 61.052 66.667 5.06 5.39 0.00 4.94
186 187 4.335647 AAGGAGCAGCACCCGTGG 62.336 66.667 5.06 0.00 0.00 4.94
213 214 3.772619 GGCACGGCCTGTCTATTAA 57.227 52.632 0.00 0.00 46.69 1.40
214 215 2.032680 GGCACGGCCTGTCTATTAAA 57.967 50.000 0.00 0.00 46.69 1.52
215 216 1.669265 GGCACGGCCTGTCTATTAAAC 59.331 52.381 0.00 0.00 46.69 2.01
216 217 2.352388 GCACGGCCTGTCTATTAAACA 58.648 47.619 0.00 0.00 0.00 2.83
217 218 2.943033 GCACGGCCTGTCTATTAAACAT 59.057 45.455 0.00 0.00 0.00 2.71
218 219 3.242739 GCACGGCCTGTCTATTAAACATG 60.243 47.826 0.00 0.00 0.00 3.21
219 220 2.943033 ACGGCCTGTCTATTAAACATGC 59.057 45.455 0.00 0.00 37.49 4.06
220 221 3.990318 GGCCTGTCTATTAAACATGCC 57.010 47.619 8.67 8.67 46.39 4.40
223 224 4.863491 GCCTGTCTATTAAACATGCCATG 58.137 43.478 2.40 2.40 33.70 3.66
224 225 4.261741 GCCTGTCTATTAAACATGCCATGG 60.262 45.833 7.63 7.63 33.70 3.66
225 226 4.261741 CCTGTCTATTAAACATGCCATGGC 60.262 45.833 30.54 30.54 42.35 4.40
250 251 4.778143 GCCGGGCCAGACACGATT 62.778 66.667 8.12 0.00 0.00 3.34
251 252 2.897207 CCGGGCCAGACACGATTA 59.103 61.111 4.39 0.00 0.00 1.75
252 253 1.227263 CCGGGCCAGACACGATTAG 60.227 63.158 4.39 0.00 0.00 1.73
253 254 1.883084 CGGGCCAGACACGATTAGC 60.883 63.158 4.39 0.00 0.00 3.09
254 255 1.220749 GGGCCAGACACGATTAGCA 59.779 57.895 4.39 0.00 0.00 3.49
255 256 1.090052 GGGCCAGACACGATTAGCAC 61.090 60.000 4.39 0.00 0.00 4.40
256 257 0.391130 GGCCAGACACGATTAGCACA 60.391 55.000 0.00 0.00 0.00 4.57
257 258 1.002366 GCCAGACACGATTAGCACAG 58.998 55.000 0.00 0.00 0.00 3.66
258 259 1.404181 GCCAGACACGATTAGCACAGA 60.404 52.381 0.00 0.00 0.00 3.41
259 260 2.263077 CCAGACACGATTAGCACAGAC 58.737 52.381 0.00 0.00 0.00 3.51
260 261 2.263077 CAGACACGATTAGCACAGACC 58.737 52.381 0.00 0.00 0.00 3.85
261 262 1.135373 AGACACGATTAGCACAGACCG 60.135 52.381 0.00 0.00 0.00 4.79
262 263 0.601558 ACACGATTAGCACAGACCGT 59.398 50.000 0.00 0.00 0.00 4.83
300 301 2.672996 CCCGTTTGGCCAGGTCTG 60.673 66.667 5.11 0.00 0.00 3.51
301 302 3.365265 CCGTTTGGCCAGGTCTGC 61.365 66.667 5.11 0.00 0.00 4.26
307 308 4.729918 GGCCAGGTCTGCCCACAG 62.730 72.222 0.00 0.00 43.33 3.66
309 310 4.729918 CCAGGTCTGCCCACAGCC 62.730 72.222 0.00 0.00 44.10 4.85
310 311 4.729918 CAGGTCTGCCCACAGCCC 62.730 72.222 0.00 0.00 42.53 5.19
312 313 4.284550 GGTCTGCCCACAGCCCAA 62.285 66.667 0.00 0.00 41.77 4.12
313 314 2.985847 GTCTGCCCACAGCCCAAC 60.986 66.667 0.00 0.00 44.10 3.77
314 315 4.284550 TCTGCCCACAGCCCAACC 62.285 66.667 0.00 0.00 44.10 3.77
315 316 4.601794 CTGCCCACAGCCCAACCA 62.602 66.667 0.00 0.00 42.71 3.67
316 317 4.912395 TGCCCACAGCCCAACCAC 62.912 66.667 0.00 0.00 42.71 4.16
318 319 4.994756 CCCACAGCCCAACCACCC 62.995 72.222 0.00 0.00 0.00 4.61
319 320 4.217210 CCACAGCCCAACCACCCA 62.217 66.667 0.00 0.00 0.00 4.51
320 321 2.123511 CACAGCCCAACCACCCAA 60.124 61.111 0.00 0.00 0.00 4.12
321 322 1.760086 CACAGCCCAACCACCCAAA 60.760 57.895 0.00 0.00 0.00 3.28
322 323 1.760480 ACAGCCCAACCACCCAAAC 60.760 57.895 0.00 0.00 0.00 2.93
323 324 2.123033 AGCCCAACCACCCAAACC 60.123 61.111 0.00 0.00 0.00 3.27
324 325 3.238497 GCCCAACCACCCAAACCC 61.238 66.667 0.00 0.00 0.00 4.11
325 326 2.612251 CCCAACCACCCAAACCCT 59.388 61.111 0.00 0.00 0.00 4.34
326 327 1.854874 CCCAACCACCCAAACCCTA 59.145 57.895 0.00 0.00 0.00 3.53
327 328 0.188834 CCCAACCACCCAAACCCTAA 59.811 55.000 0.00 0.00 0.00 2.69
328 329 1.334160 CCAACCACCCAAACCCTAAC 58.666 55.000 0.00 0.00 0.00 2.34
329 330 1.133294 CCAACCACCCAAACCCTAACT 60.133 52.381 0.00 0.00 0.00 2.24
330 331 2.235891 CAACCACCCAAACCCTAACTC 58.764 52.381 0.00 0.00 0.00 3.01
331 332 1.525175 ACCACCCAAACCCTAACTCA 58.475 50.000 0.00 0.00 0.00 3.41
332 333 1.423921 ACCACCCAAACCCTAACTCAG 59.576 52.381 0.00 0.00 0.00 3.35
687 688 0.977627 ACCCATCCACAGATCGAGCA 60.978 55.000 2.38 0.00 0.00 4.26
698 699 2.317149 GATCGAGCAAGGGGTGAGGG 62.317 65.000 0.00 0.00 0.00 4.30
715 716 3.785859 GAGCGCCCAGATCCACCA 61.786 66.667 2.29 0.00 0.00 4.17
720 721 1.692749 GCCCAGATCCACCACCCTA 60.693 63.158 0.00 0.00 0.00 3.53
724 725 1.285280 CAGATCCACCACCCTACCAA 58.715 55.000 0.00 0.00 0.00 3.67
727 728 2.041216 AGATCCACCACCCTACCAAAAC 59.959 50.000 0.00 0.00 0.00 2.43
733 734 3.055675 CACCACCCTACCAAAACGAGATA 60.056 47.826 0.00 0.00 0.00 1.98
753 754 1.630878 ACAACACCAGATCCCTCCTTC 59.369 52.381 0.00 0.00 0.00 3.46
762 763 2.317594 AGATCCCTCCTTCTTCCTGACT 59.682 50.000 0.00 0.00 0.00 3.41
768 769 1.625818 TCCTTCTTCCTGACTTCTGGC 59.374 52.381 0.00 0.00 35.24 4.85
769 770 1.349026 CCTTCTTCCTGACTTCTGGCA 59.651 52.381 0.00 0.00 35.24 4.92
770 771 2.421619 CTTCTTCCTGACTTCTGGCAC 58.578 52.381 0.00 0.00 35.24 5.01
786 790 4.250305 ACCGTCGCAGCCACCTTT 62.250 61.111 0.00 0.00 0.00 3.11
787 791 2.978010 CCGTCGCAGCCACCTTTT 60.978 61.111 0.00 0.00 0.00 2.27
791 795 1.070105 TCGCAGCCACCTTTTACGT 59.930 52.632 0.00 0.00 0.00 3.57
792 796 0.947180 TCGCAGCCACCTTTTACGTC 60.947 55.000 0.00 0.00 0.00 4.34
808 812 1.511768 GTCGCGGCTCTCCTACTTT 59.488 57.895 1.90 0.00 0.00 2.66
820 824 1.749634 TCCTACTTTGTCTAGCCTCGC 59.250 52.381 0.00 0.00 0.00 5.03
822 826 1.132643 CTACTTTGTCTAGCCTCGCGT 59.867 52.381 5.77 0.00 0.00 6.01
891 899 2.100197 CTTGTCGGACTCACCATCCTA 58.900 52.381 9.88 0.00 38.90 2.94
892 900 2.454336 TGTCGGACTCACCATCCTAT 57.546 50.000 9.88 0.00 38.90 2.57
925 933 3.589654 ATGGGCGTGTGTGAGTCCG 62.590 63.158 0.00 0.00 34.21 4.79
970 978 2.275418 GTGGCGGTGATGGGGAAT 59.725 61.111 0.00 0.00 0.00 3.01
979 987 2.224523 GGTGATGGGGAATAAGATCGCA 60.225 50.000 0.00 0.00 34.19 5.10
1034 1043 2.759973 CGAGCTGCCCTCCACCTA 60.760 66.667 0.00 0.00 37.27 3.08
1045 1054 1.254026 CTCCACCTACAACCTCGTGA 58.746 55.000 0.00 0.00 0.00 4.35
1050 1059 1.623811 ACCTACAACCTCGTGATGCTT 59.376 47.619 0.00 0.00 0.00 3.91
1062 1071 0.247460 TGATGCTTGACCTCGTCAGG 59.753 55.000 0.00 0.00 43.69 3.86
1065 1074 2.651361 CTTGACCTCGTCAGGCGT 59.349 61.111 0.00 0.00 45.05 5.68
1087 1096 1.591703 CGCCTCCTCTACAAGCACA 59.408 57.895 0.00 0.00 0.00 4.57
1089 1098 1.406069 CGCCTCCTCTACAAGCACAAT 60.406 52.381 0.00 0.00 0.00 2.71
1101 1110 2.361610 CACAATGAGGGCCGCCTT 60.362 61.111 9.86 0.00 0.00 4.35
1111 1120 2.261671 GCCGCCTTCTCGTCAAGA 59.738 61.111 0.00 0.00 0.00 3.02
1126 1135 2.280183 GTCAAGATCTACTTCAAGCGCG 59.720 50.000 0.00 0.00 36.61 6.86
1159 1168 1.449778 GAGCTCAAGGTAACCGCCC 60.450 63.158 9.40 0.00 37.17 6.13
1166 1175 1.921869 AAGGTAACCGCCCCATCCAG 61.922 60.000 0.00 0.00 37.17 3.86
1172 1181 4.320456 CGCCCCATCCAGATCCCG 62.320 72.222 0.00 0.00 0.00 5.14
1191 1200 2.086194 TTCCCCCTTCGGTTTGGGT 61.086 57.895 0.00 0.00 41.82 4.51
1194 1203 2.518933 CCCTTCGGTTTGGGTGGT 59.481 61.111 0.00 0.00 38.65 4.16
1195 1204 1.901464 CCCTTCGGTTTGGGTGGTG 60.901 63.158 0.00 0.00 38.65 4.17
1196 1205 1.149627 CCTTCGGTTTGGGTGGTGA 59.850 57.895 0.00 0.00 0.00 4.02
1198 1207 1.515521 CTTCGGTTTGGGTGGTGAGC 61.516 60.000 0.00 0.00 0.00 4.26
1199 1208 3.353836 CGGTTTGGGTGGTGAGCG 61.354 66.667 0.00 0.00 0.00 5.03
1201 1210 2.258726 GGTTTGGGTGGTGAGCGAC 61.259 63.158 0.00 0.00 0.00 5.19
1202 1211 2.280524 TTTGGGTGGTGAGCGACG 60.281 61.111 0.00 0.00 0.00 5.12
1209 1219 0.388649 GTGGTGAGCGACGTGAGAAT 60.389 55.000 0.00 0.00 0.00 2.40
1222 1232 5.444613 CGACGTGAGAATATCTGTTTGTTGG 60.445 44.000 0.00 0.00 0.00 3.77
1227 1237 6.094603 GTGAGAATATCTGTTTGTTGGCTCAT 59.905 38.462 0.00 0.00 32.20 2.90
1238 1248 2.779430 TGTTGGCTCATAGGACCATGAT 59.221 45.455 0.00 0.00 34.50 2.45
1275 1285 2.606519 CGGAGGGTGTTCCAGGGA 60.607 66.667 0.00 0.00 37.05 4.20
1291 1301 1.152525 GGACTCGAGGGCTCCCATA 60.153 63.158 18.41 0.00 38.92 2.74
1296 1306 0.542938 TCGAGGGCTCCCATATCTGG 60.543 60.000 7.82 0.00 42.73 3.86
1303 1313 0.695347 CTCCCATATCTGGCCCTTCC 59.305 60.000 0.00 0.00 41.64 3.46
1322 1332 7.545615 GCCCTTCCAGTGTTTAATTTTTCATAG 59.454 37.037 0.00 0.00 0.00 2.23
1348 1358 8.699749 GTCAGGTTGTAATAATTTTCAACTTGC 58.300 33.333 15.72 10.81 43.55 4.01
1360 1370 2.419057 AACTTGCAGTCAGGTTGCC 58.581 52.632 0.00 0.00 40.42 4.52
1361 1371 0.106519 AACTTGCAGTCAGGTTGCCT 60.107 50.000 0.00 0.00 40.42 4.75
1388 1398 7.039293 TGCTCTCAGTCACTTGGTAGTTTTATA 60.039 37.037 0.00 0.00 30.26 0.98
1456 1466 4.583871 AGATAAGGAACACAAAGCAGAGG 58.416 43.478 0.00 0.00 0.00 3.69
1499 1510 7.234355 TCACTGCATAATCTGATAGACCTAGA 58.766 38.462 0.00 0.00 0.00 2.43
1506 1517 3.161067 TCTGATAGACCTAGATGGCAGC 58.839 50.000 0.00 0.00 40.22 5.25
1531 1542 8.500773 GCAGTGTAGTAAGCAAAACATTAACTA 58.499 33.333 0.00 0.00 0.00 2.24
1535 1546 9.004717 TGTAGTAAGCAAAACATTAACTATGCA 57.995 29.630 0.00 0.00 37.81 3.96
1551 1562 2.113860 TGCAATGCTTCCAGTAGACC 57.886 50.000 6.82 0.00 0.00 3.85
1560 1571 3.637229 GCTTCCAGTAGACCACTAGCATA 59.363 47.826 0.00 0.00 36.68 3.14
1642 1653 6.119536 TGATAAGTTAAACCTAGGTGCATGG 58.880 40.000 17.14 0.00 0.00 3.66
1693 1704 4.486839 ACTGTACCTGTGTACTAAACCCT 58.513 43.478 4.68 0.00 46.19 4.34
1720 1731 7.776969 AGTTAAGTATACCCGAGTATTCTCACA 59.223 37.037 0.00 0.00 39.88 3.58
1723 1734 5.764192 AGTATACCCGAGTATTCTCACACTC 59.236 44.000 0.00 0.00 39.88 3.51
1742 1753 5.693555 ACACTCGCATAATATGTGTGATCTG 59.306 40.000 18.88 11.20 39.90 2.90
1768 1780 7.093684 GGGTTTCAGTTGGCCTTGTATTTATAA 60.094 37.037 3.32 0.00 0.00 0.98
1773 1785 9.474313 TCAGTTGGCCTTGTATTTATAATTTCT 57.526 29.630 3.32 0.00 0.00 2.52
1802 1814 3.773860 ATCGTTCTGCTAGTCTCACTG 57.226 47.619 0.00 0.00 0.00 3.66
1825 1837 3.007614 TGGTTAGCTCTAACAACCCAGTC 59.992 47.826 18.23 3.00 45.32 3.51
1849 1861 5.431765 CAGTATTTCAGTTATGGAGTGGCT 58.568 41.667 0.00 0.00 0.00 4.75
1989 2003 9.520204 GTGCAGTAAACATTATATGCAAGATTT 57.480 29.630 11.88 0.00 44.43 2.17
2049 2064 7.051000 TGGTTAATGTCAATCAATACCGATCA 58.949 34.615 0.00 0.00 31.75 2.92
2060 2075 0.535335 TACCGATCAAGGTGACTGGC 59.465 55.000 2.76 0.00 45.54 4.85
2087 2102 4.395854 TCAACATTTGCTAGAATCGTGCAT 59.604 37.500 0.00 0.00 36.55 3.96
2093 2108 0.855349 CTAGAATCGTGCATCGTGCC 59.145 55.000 7.38 0.00 44.23 5.01
2183 2198 6.670233 ACAAAAATGGTAATGCATTTTGCTG 58.330 32.000 18.75 8.93 45.31 4.41
2233 2248 0.618680 TGCTCATACCAGGGTGCTCT 60.619 55.000 0.06 0.00 0.00 4.09
2247 2262 6.042093 CCAGGGTGCTCTATTTAGTCTATTGA 59.958 42.308 0.00 0.00 0.00 2.57
2267 2282 7.976135 ATTGAGAATGCTAATAGACCATGAC 57.024 36.000 0.00 0.00 0.00 3.06
2307 2322 1.981495 CCCCCTCTCTCTGTTTGACTT 59.019 52.381 0.00 0.00 0.00 3.01
2312 2327 2.985809 CTCTCTCTGTTTGACTTGCTCG 59.014 50.000 0.00 0.00 0.00 5.03
2335 2350 5.239306 CGATCTCTCTCTATCTTTCTGCAGT 59.761 44.000 14.67 0.00 0.00 4.40
2422 2437 0.533531 GCTCCGCATGGATCATGACA 60.534 55.000 11.57 0.00 45.33 3.58
2432 2447 0.855349 GATCATGACATGGTCGTCGC 59.145 55.000 12.82 0.00 38.84 5.19
2513 2528 1.228862 ATGGTTCACCCTGGGTTGC 60.229 57.895 17.76 9.05 31.02 4.17
2594 2609 3.056749 GCTTAGGCGGCTTAGCTTAGATA 60.057 47.826 34.26 4.71 37.29 1.98
2622 2637 3.448093 TGTGATGCTCATTTTGGGGTA 57.552 42.857 0.00 0.00 0.00 3.69
2722 2737 3.643237 AGCTGTAGATAGGCAAGGTACA 58.357 45.455 0.00 0.00 0.00 2.90
2810 2826 3.243359 TCTGGGAAAGCAAAGGTGATT 57.757 42.857 0.00 0.00 33.93 2.57
2857 2873 2.040544 GCCGTGTGTGGGGATTCAG 61.041 63.158 0.00 0.00 0.00 3.02
2887 2903 3.494251 CAGTCGTGTGTGATTGATGTCAA 59.506 43.478 0.00 0.00 40.51 3.18
2952 2968 6.539649 TTGTTGTGCACTACTGAAGTTATC 57.460 37.500 27.40 2.67 35.76 1.75
2996 3012 8.747538 ACTAAACTTGTACAATTCTTGTCCTT 57.252 30.769 9.13 0.00 44.12 3.36
3055 3071 8.674263 TCTGAATGTTTTGCCAATTTTTATGT 57.326 26.923 0.00 0.00 0.00 2.29
3062 3078 5.798125 TTGCCAATTTTTATGTCCTGTGA 57.202 34.783 0.00 0.00 0.00 3.58
3080 3096 2.926838 GTGAGCTAGCAAACTGAGCTAC 59.073 50.000 18.83 0.00 46.42 3.58
3112 3128 6.368805 TCATCTCTGTCCTTCAGCTTCTATA 58.631 40.000 0.00 0.00 43.32 1.31
3184 3200 7.770433 TGGTTTCAATCGATATTTGTCTCATCT 59.230 33.333 0.00 0.00 0.00 2.90
3222 3238 8.650143 ATCAGTATGTTGTTTTAACCCTGATT 57.350 30.769 0.00 0.00 34.44 2.57
3319 3336 5.242838 TGGTTTACCCATGTCAGATTTGTTC 59.757 40.000 0.00 0.00 38.72 3.18
3394 3411 6.931840 AGCTCTACTTTATGCTAATACTTGCC 59.068 38.462 0.00 0.00 33.64 4.52
3396 3413 7.442666 GCTCTACTTTATGCTAATACTTGCCTT 59.557 37.037 0.00 0.00 0.00 4.35
3412 3429 5.821995 ACTTGCCTTTGTAACATTTTGCATT 59.178 32.000 0.00 0.00 0.00 3.56
3414 3431 4.024218 TGCCTTTGTAACATTTTGCATTGC 60.024 37.500 0.46 0.46 0.00 3.56
3442 3459 5.079689 TCTAAATGGACAAGTACATGCGA 57.920 39.130 0.00 0.00 33.62 5.10
3443 3460 5.670485 TCTAAATGGACAAGTACATGCGAT 58.330 37.500 0.00 0.00 33.62 4.58
3453 3470 3.396560 AGTACATGCGATGTCCATCATG 58.603 45.455 7.94 7.51 43.67 3.07
3474 3491 4.864633 TGAACGATGATGCAGACTAGATC 58.135 43.478 0.00 0.00 0.00 2.75
3476 3493 5.765182 TGAACGATGATGCAGACTAGATCTA 59.235 40.000 1.69 1.69 35.15 1.98
3482 3499 7.095017 CGATGATGCAGACTAGATCTACAACTA 60.095 40.741 0.00 0.00 34.24 2.24
3501 3518 6.070251 ACAACTACAGAACCATCCATCACATA 60.070 38.462 0.00 0.00 0.00 2.29
3548 3565 2.107950 TGTTGAACAGATAAGGGCCG 57.892 50.000 0.00 0.00 0.00 6.13
3549 3566 1.626321 TGTTGAACAGATAAGGGCCGA 59.374 47.619 0.00 0.00 0.00 5.54
3568 3585 2.880268 CGAATGCTTGATGGCCTTATGA 59.120 45.455 3.32 0.00 0.00 2.15
3590 3607 5.823570 TGATTGATGCATGTATCATGTGACA 59.176 36.000 24.52 16.72 36.97 3.58
3591 3608 5.488645 TTGATGCATGTATCATGTGACAC 57.511 39.130 24.52 0.00 36.97 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.196901 GGTTGGTTTTTAGGCCTATTGGG 59.803 47.826 14.74 0.00 38.36 4.12
66 67 4.093743 AGGTTGGTTTTTAGGCCTATTGG 58.906 43.478 14.74 0.00 0.00 3.16
67 68 5.163550 GCTAGGTTGGTTTTTAGGCCTATTG 60.164 44.000 14.74 0.00 0.00 1.90
68 69 4.954202 GCTAGGTTGGTTTTTAGGCCTATT 59.046 41.667 14.74 0.00 0.00 1.73
69 70 4.017867 TGCTAGGTTGGTTTTTAGGCCTAT 60.018 41.667 14.74 0.00 0.00 2.57
70 71 3.331294 TGCTAGGTTGGTTTTTAGGCCTA 59.669 43.478 8.91 8.91 0.00 3.93
71 72 2.109304 TGCTAGGTTGGTTTTTAGGCCT 59.891 45.455 11.78 11.78 0.00 5.19
72 73 2.492088 CTGCTAGGTTGGTTTTTAGGCC 59.508 50.000 0.00 0.00 0.00 5.19
73 74 2.492088 CCTGCTAGGTTGGTTTTTAGGC 59.508 50.000 0.00 0.00 0.00 3.93
74 75 2.492088 GCCTGCTAGGTTGGTTTTTAGG 59.508 50.000 4.45 0.00 37.80 2.69
75 76 3.191371 CAGCCTGCTAGGTTGGTTTTTAG 59.809 47.826 9.98 0.00 42.16 1.85
76 77 3.153919 CAGCCTGCTAGGTTGGTTTTTA 58.846 45.455 9.98 0.00 42.16 1.52
77 78 1.963515 CAGCCTGCTAGGTTGGTTTTT 59.036 47.619 9.98 0.00 42.16 1.94
78 79 1.144913 TCAGCCTGCTAGGTTGGTTTT 59.855 47.619 15.38 0.00 45.40 2.43
79 80 0.771127 TCAGCCTGCTAGGTTGGTTT 59.229 50.000 15.38 0.00 45.40 3.27
80 81 0.771127 TTCAGCCTGCTAGGTTGGTT 59.229 50.000 15.38 0.00 45.40 3.67
81 82 0.771127 TTTCAGCCTGCTAGGTTGGT 59.229 50.000 15.38 0.00 45.40 3.67
82 83 1.909700 TTTTCAGCCTGCTAGGTTGG 58.090 50.000 15.38 2.89 45.40 3.77
83 84 2.821969 ACATTTTCAGCCTGCTAGGTTG 59.178 45.455 11.15 11.15 46.54 3.77
84 85 2.821969 CACATTTTCAGCCTGCTAGGTT 59.178 45.455 0.00 0.00 37.80 3.50
85 86 2.440409 CACATTTTCAGCCTGCTAGGT 58.560 47.619 0.00 0.00 37.80 3.08
86 87 1.133790 GCACATTTTCAGCCTGCTAGG 59.866 52.381 0.00 0.00 38.80 3.02
87 88 1.814394 TGCACATTTTCAGCCTGCTAG 59.186 47.619 0.00 0.00 0.00 3.42
88 89 1.814394 CTGCACATTTTCAGCCTGCTA 59.186 47.619 0.00 0.00 0.00 3.49
89 90 0.601558 CTGCACATTTTCAGCCTGCT 59.398 50.000 0.00 0.00 0.00 4.24
90 91 3.117589 CTGCACATTTTCAGCCTGC 57.882 52.632 0.00 0.00 0.00 4.85
95 96 0.389426 GCTGGGCTGCACATTTTCAG 60.389 55.000 4.43 0.00 0.00 3.02
96 97 1.667151 GCTGGGCTGCACATTTTCA 59.333 52.632 4.43 0.00 0.00 2.69
97 98 1.444895 CGCTGGGCTGCACATTTTC 60.445 57.895 4.43 0.00 0.00 2.29
98 99 2.202395 ACGCTGGGCTGCACATTTT 61.202 52.632 4.43 0.00 0.00 1.82
99 100 2.598394 ACGCTGGGCTGCACATTT 60.598 55.556 4.43 0.00 0.00 2.32
100 101 3.367743 CACGCTGGGCTGCACATT 61.368 61.111 4.43 0.00 0.00 2.71
104 105 3.841137 TTTAGCACGCTGGGCTGCA 62.841 57.895 14.30 0.00 42.62 4.41
105 106 3.055719 TTTAGCACGCTGGGCTGC 61.056 61.111 14.30 9.91 42.62 5.25
106 107 2.870372 GTTTAGCACGCTGGGCTG 59.130 61.111 14.30 0.00 42.62 4.85
107 108 2.742372 CGTTTAGCACGCTGGGCT 60.742 61.111 10.07 10.07 43.37 5.19
115 116 2.469516 CCGATGGCCCGTTTAGCAC 61.470 63.158 0.00 0.00 0.00 4.40
116 117 2.124901 CCGATGGCCCGTTTAGCA 60.125 61.111 0.00 0.00 0.00 3.49
117 118 2.900337 CCCGATGGCCCGTTTAGC 60.900 66.667 0.00 0.00 0.00 3.09
133 134 1.153107 ATTAGTAAACGGGCCGGCC 60.153 57.895 38.57 38.57 0.00 6.13
134 135 0.462403 TGATTAGTAAACGGGCCGGC 60.462 55.000 31.78 21.18 0.00 6.13
135 136 1.578583 CTGATTAGTAAACGGGCCGG 58.421 55.000 31.78 12.53 0.00 6.13
136 137 1.578583 CCTGATTAGTAAACGGGCCG 58.421 55.000 27.06 27.06 0.00 6.13
137 138 1.306148 GCCTGATTAGTAAACGGGCC 58.694 55.000 25.41 12.20 46.61 5.80
139 140 1.134610 ACGGCCTGATTAGTAAACGGG 60.135 52.381 12.58 12.58 0.00 5.28
140 141 1.931172 CACGGCCTGATTAGTAAACGG 59.069 52.381 0.00 0.00 0.00 4.44
141 142 1.326548 GCACGGCCTGATTAGTAAACG 59.673 52.381 0.00 0.00 0.00 3.60
142 143 1.669265 GGCACGGCCTGATTAGTAAAC 59.331 52.381 0.00 0.00 46.69 2.01
143 144 2.032680 GGCACGGCCTGATTAGTAAA 57.967 50.000 0.00 0.00 46.69 2.01
144 145 3.772619 GGCACGGCCTGATTAGTAA 57.227 52.632 0.00 0.00 46.69 2.24
162 163 4.355720 TGCTGCTCCTTGGCCCAG 62.356 66.667 0.00 0.00 0.00 4.45
163 164 4.666253 GTGCTGCTCCTTGGCCCA 62.666 66.667 0.00 0.00 0.00 5.36
167 168 4.335647 ACGGGTGCTGCTCCTTGG 62.336 66.667 19.07 11.69 0.00 3.61
168 169 3.052082 CACGGGTGCTGCTCCTTG 61.052 66.667 19.07 14.33 0.00 3.61
169 170 4.335647 CCACGGGTGCTGCTCCTT 62.336 66.667 19.07 5.31 0.00 3.36
196 197 2.352388 TGTTTAATAGACAGGCCGTGC 58.648 47.619 4.94 0.00 0.00 5.34
197 198 3.242739 GCATGTTTAATAGACAGGCCGTG 60.243 47.826 9.05 2.95 45.91 4.94
198 199 2.943033 GCATGTTTAATAGACAGGCCGT 59.057 45.455 9.05 0.00 45.91 5.68
199 200 3.609103 GCATGTTTAATAGACAGGCCG 57.391 47.619 9.05 0.00 45.91 6.13
202 203 4.261741 GCCATGGCATGTTTAATAGACAGG 60.262 45.833 32.08 6.97 41.49 4.00
203 204 4.863491 GCCATGGCATGTTTAATAGACAG 58.137 43.478 32.08 7.10 41.49 3.51
204 205 4.916983 GCCATGGCATGTTTAATAGACA 57.083 40.909 32.08 0.00 41.49 3.41
233 234 3.379865 TAATCGTGTCTGGCCCGGC 62.380 63.158 0.00 0.00 0.00 6.13
234 235 1.227263 CTAATCGTGTCTGGCCCGG 60.227 63.158 0.00 0.00 0.00 5.73
235 236 1.883084 GCTAATCGTGTCTGGCCCG 60.883 63.158 0.00 0.00 0.00 6.13
236 237 1.090052 GTGCTAATCGTGTCTGGCCC 61.090 60.000 0.00 0.00 0.00 5.80
237 238 0.391130 TGTGCTAATCGTGTCTGGCC 60.391 55.000 0.00 0.00 0.00 5.36
238 239 1.002366 CTGTGCTAATCGTGTCTGGC 58.998 55.000 0.00 0.00 0.00 4.85
239 240 2.263077 GTCTGTGCTAATCGTGTCTGG 58.737 52.381 0.00 0.00 0.00 3.86
240 241 2.263077 GGTCTGTGCTAATCGTGTCTG 58.737 52.381 0.00 0.00 0.00 3.51
241 242 1.135373 CGGTCTGTGCTAATCGTGTCT 60.135 52.381 0.00 0.00 0.00 3.41
242 243 1.269166 CGGTCTGTGCTAATCGTGTC 58.731 55.000 0.00 0.00 0.00 3.67
243 244 0.601558 ACGGTCTGTGCTAATCGTGT 59.398 50.000 0.00 0.00 0.00 4.49
244 245 0.992072 CACGGTCTGTGCTAATCGTG 59.008 55.000 0.00 0.00 42.70 4.35
245 246 3.418675 CACGGTCTGTGCTAATCGT 57.581 52.632 0.00 0.00 42.70 3.73
283 284 2.672996 CAGACCTGGCCAAACGGG 60.673 66.667 7.01 7.12 42.81 5.28
284 285 3.365265 GCAGACCTGGCCAAACGG 61.365 66.667 7.01 7.56 0.00 4.44
292 293 4.729918 GGCTGTGGGCAGACCTGG 62.730 72.222 0.00 0.00 44.95 4.45
297 298 4.284550 GGTTGGGCTGTGGGCAGA 62.285 66.667 0.00 0.00 45.28 4.26
298 299 4.601794 TGGTTGGGCTGTGGGCAG 62.602 66.667 0.00 0.00 45.23 4.85
299 300 4.912395 GTGGTTGGGCTGTGGGCA 62.912 66.667 0.00 0.00 44.01 5.36
301 302 4.994756 GGGTGGTTGGGCTGTGGG 62.995 72.222 0.00 0.00 0.00 4.61
302 303 3.747521 TTGGGTGGTTGGGCTGTGG 62.748 63.158 0.00 0.00 0.00 4.17
303 304 1.760086 TTTGGGTGGTTGGGCTGTG 60.760 57.895 0.00 0.00 0.00 3.66
304 305 1.760480 GTTTGGGTGGTTGGGCTGT 60.760 57.895 0.00 0.00 0.00 4.40
305 306 2.506957 GGTTTGGGTGGTTGGGCTG 61.507 63.158 0.00 0.00 0.00 4.85
306 307 2.123033 GGTTTGGGTGGTTGGGCT 60.123 61.111 0.00 0.00 0.00 5.19
307 308 2.374781 TAGGGTTTGGGTGGTTGGGC 62.375 60.000 0.00 0.00 0.00 5.36
308 309 0.188834 TTAGGGTTTGGGTGGTTGGG 59.811 55.000 0.00 0.00 0.00 4.12
309 310 1.133294 AGTTAGGGTTTGGGTGGTTGG 60.133 52.381 0.00 0.00 0.00 3.77
310 311 2.235891 GAGTTAGGGTTTGGGTGGTTG 58.764 52.381 0.00 0.00 0.00 3.77
311 312 1.854280 TGAGTTAGGGTTTGGGTGGTT 59.146 47.619 0.00 0.00 0.00 3.67
312 313 1.423921 CTGAGTTAGGGTTTGGGTGGT 59.576 52.381 0.00 0.00 0.00 4.16
313 314 2.200373 CTGAGTTAGGGTTTGGGTGG 57.800 55.000 0.00 0.00 0.00 4.61
649 650 2.856039 TACAGGAGAGGGTGGAGCGG 62.856 65.000 0.00 0.00 0.00 5.52
650 651 1.379977 TACAGGAGAGGGTGGAGCG 60.380 63.158 0.00 0.00 0.00 5.03
665 666 2.031870 CTCGATCTGTGGATGGGTACA 58.968 52.381 0.00 0.00 31.46 2.90
698 699 3.785859 TGGTGGATCTGGGCGCTC 61.786 66.667 7.64 2.47 0.00 5.03
713 714 2.781681 ATCTCGTTTTGGTAGGGTGG 57.218 50.000 0.00 0.00 0.00 4.61
715 716 4.040706 TGTTGTATCTCGTTTTGGTAGGGT 59.959 41.667 0.00 0.00 0.00 4.34
720 721 3.811083 TGGTGTTGTATCTCGTTTTGGT 58.189 40.909 0.00 0.00 0.00 3.67
724 725 4.504858 GGATCTGGTGTTGTATCTCGTTT 58.495 43.478 0.00 0.00 0.00 3.60
727 728 2.695666 AGGGATCTGGTGTTGTATCTCG 59.304 50.000 0.00 0.00 0.00 4.04
733 734 1.630878 GAAGGAGGGATCTGGTGTTGT 59.369 52.381 0.00 0.00 0.00 3.32
753 754 0.671781 CGGTGCCAGAAGTCAGGAAG 60.672 60.000 0.00 0.00 0.00 3.46
768 769 4.988598 AAGGTGGCTGCGACGGTG 62.989 66.667 8.69 0.00 0.00 4.94
769 770 2.386064 TAAAAGGTGGCTGCGACGGT 62.386 55.000 8.69 0.00 0.00 4.83
770 771 1.669760 TAAAAGGTGGCTGCGACGG 60.670 57.895 8.69 0.00 0.00 4.79
786 790 1.450134 TAGGAGAGCCGCGACGTAA 60.450 57.895 8.23 0.00 39.96 3.18
787 791 2.176273 GTAGGAGAGCCGCGACGTA 61.176 63.158 8.23 0.00 39.96 3.57
791 795 1.248785 ACAAAGTAGGAGAGCCGCGA 61.249 55.000 8.23 0.00 39.96 5.87
792 796 0.802607 GACAAAGTAGGAGAGCCGCG 60.803 60.000 0.00 0.00 39.96 6.46
808 812 2.360726 TGGACGCGAGGCTAGACA 60.361 61.111 15.93 0.00 40.87 3.41
866 874 1.666011 GTGAGTCCGACAAGAGGCA 59.334 57.895 0.40 0.00 0.00 4.75
870 878 0.895530 GGATGGTGAGTCCGACAAGA 59.104 55.000 0.40 0.00 39.52 3.02
873 881 2.031870 CATAGGATGGTGAGTCCGACA 58.968 52.381 0.40 0.00 40.76 4.35
891 899 0.395311 CCATCTCCTTGGTGCAGCAT 60.395 55.000 20.91 0.00 31.74 3.79
892 900 1.001764 CCATCTCCTTGGTGCAGCA 60.002 57.895 15.99 15.99 31.74 4.41
954 962 0.182537 CTTATTCCCCATCACCGCCA 59.817 55.000 0.00 0.00 0.00 5.69
970 978 0.245266 TGCGTTGTCCTGCGATCTTA 59.755 50.000 0.00 0.00 0.00 2.10
979 987 4.379243 CGAGGCCTGCGTTGTCCT 62.379 66.667 12.00 0.00 0.00 3.85
1003 1012 1.153745 GCTCGTGCAGGTAGGACTG 60.154 63.158 6.26 0.00 41.41 3.51
1017 1026 2.759973 TAGGTGGAGGGCAGCTCG 60.760 66.667 0.00 0.00 0.00 5.03
1020 1029 1.377333 GTTGTAGGTGGAGGGCAGC 60.377 63.158 0.00 0.00 0.00 5.25
1034 1043 1.512926 GTCAAGCATCACGAGGTTGT 58.487 50.000 0.00 0.00 43.08 3.32
1045 1054 1.078848 GCCTGACGAGGTCAAGCAT 60.079 57.895 12.99 0.00 45.85 3.79
1050 1059 3.680786 CCACGCCTGACGAGGTCA 61.681 66.667 0.00 0.00 46.21 4.02
1065 1074 2.284331 TTGTAGAGGAGGCGGCCA 60.284 61.111 23.09 0.00 0.00 5.36
1067 1076 2.202946 GCTTGTAGAGGAGGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
1079 1088 1.973281 CGGCCCTCATTGTGCTTGT 60.973 57.895 0.00 0.00 0.00 3.16
1087 1096 2.592308 GAGAAGGCGGCCCTCATT 59.408 61.111 19.30 5.65 41.90 2.57
1097 1106 4.142359 TGAAGTAGATCTTGACGAGAAGGC 60.142 45.833 0.00 0.00 38.06 4.35
1101 1110 4.437524 CGCTTGAAGTAGATCTTGACGAGA 60.438 45.833 0.00 0.00 39.13 4.04
1111 1120 1.878522 CGGCGCGCTTGAAGTAGAT 60.879 57.895 32.29 0.00 0.00 1.98
1143 1152 2.437895 GGGGCGGTTACCTTGAGC 60.438 66.667 0.00 0.00 0.00 4.26
1159 1168 1.451936 GGGAACGGGATCTGGATGG 59.548 63.158 0.00 0.00 0.00 3.51
1166 1175 2.504519 CGAAGGGGGAACGGGATC 59.495 66.667 0.00 0.00 0.00 3.36
1191 1200 1.170442 TATTCTCACGTCGCTCACCA 58.830 50.000 0.00 0.00 0.00 4.17
1194 1203 2.683362 ACAGATATTCTCACGTCGCTCA 59.317 45.455 0.00 0.00 0.00 4.26
1195 1204 3.341857 ACAGATATTCTCACGTCGCTC 57.658 47.619 0.00 0.00 0.00 5.03
1196 1205 3.784701 AACAGATATTCTCACGTCGCT 57.215 42.857 0.00 0.00 0.00 4.93
1198 1207 5.444613 CCAACAAACAGATATTCTCACGTCG 60.445 44.000 0.00 0.00 0.00 5.12
1199 1208 5.671329 GCCAACAAACAGATATTCTCACGTC 60.671 44.000 0.00 0.00 0.00 4.34
1201 1210 4.393062 AGCCAACAAACAGATATTCTCACG 59.607 41.667 0.00 0.00 0.00 4.35
1202 1211 5.412594 TGAGCCAACAAACAGATATTCTCAC 59.587 40.000 0.00 0.00 0.00 3.51
1209 1219 5.428253 GTCCTATGAGCCAACAAACAGATA 58.572 41.667 0.00 0.00 0.00 1.98
1222 1232 2.300152 TCCGAATCATGGTCCTATGAGC 59.700 50.000 9.10 0.00 40.16 4.26
1227 1237 1.048601 GCCTCCGAATCATGGTCCTA 58.951 55.000 0.00 0.00 0.00 2.94
1238 1248 1.680522 GATCTGCTCCAGCCTCCGAA 61.681 60.000 0.00 0.00 41.18 4.30
1265 1275 1.609501 CCCTCGAGTCCCTGGAACA 60.610 63.158 12.31 0.00 0.00 3.18
1275 1285 0.485099 AGATATGGGAGCCCTCGAGT 59.515 55.000 12.31 0.00 36.94 4.18
1296 1306 5.606505 TGAAAAATTAAACACTGGAAGGGC 58.393 37.500 0.00 0.00 45.89 5.19
1303 1313 9.965824 AACCTGACTATGAAAAATTAAACACTG 57.034 29.630 0.00 0.00 0.00 3.66
1322 1332 8.699749 GCAAGTTGAAAATTATTACAACCTGAC 58.300 33.333 19.86 12.57 42.05 3.51
1348 1358 0.250640 AGAGCAAGGCAACCTGACTG 60.251 55.000 0.00 0.00 31.94 3.51
1360 1370 2.540265 ACCAAGTGACTGAGAGCAAG 57.460 50.000 0.00 0.00 0.00 4.01
1361 1371 2.965831 ACTACCAAGTGACTGAGAGCAA 59.034 45.455 0.00 0.00 33.57 3.91
1395 1405 4.051922 GCGGACGATAGAATCAAAGTGAT 58.948 43.478 0.00 0.00 38.07 3.06
1399 1409 2.797156 CAGGCGGACGATAGAATCAAAG 59.203 50.000 0.00 0.00 41.38 2.77
1400 1410 2.483013 CCAGGCGGACGATAGAATCAAA 60.483 50.000 0.00 0.00 41.38 2.69
1412 1422 4.154347 CCTCTGAGCCAGGCGGAC 62.154 72.222 5.55 2.45 31.51 4.79
1456 1466 5.278266 GCAGTGAGGATGTCTGATCTACTAC 60.278 48.000 0.00 0.00 0.00 2.73
1499 1510 1.278985 TGCTTACTACACTGCTGCCAT 59.721 47.619 0.00 0.00 0.00 4.40
1535 1546 3.118592 GCTAGTGGTCTACTGGAAGCATT 60.119 47.826 3.78 0.00 40.06 3.56
1551 1562 6.751514 TTACCCAAAACATGTATGCTAGTG 57.248 37.500 0.00 0.00 0.00 2.74
1560 1571 7.818930 CAGCTAAATTGATTACCCAAAACATGT 59.181 33.333 0.00 0.00 0.00 3.21
1659 1670 7.198306 ACACAGGTACAGTTTAAAAGCATAC 57.802 36.000 0.00 0.00 0.00 2.39
1693 1704 9.277783 GTGAGAATACTCGGGTATACTTAACTA 57.722 37.037 8.72 0.00 45.25 2.24
1720 1731 5.233225 CCAGATCACACATATTATGCGAGT 58.767 41.667 3.52 0.00 0.00 4.18
1723 1734 4.318332 ACCCAGATCACACATATTATGCG 58.682 43.478 3.52 0.00 0.00 4.73
1739 1750 0.555769 AAGGCCAACTGAAACCCAGA 59.444 50.000 5.01 0.00 45.78 3.86
1742 1753 1.989706 TACAAGGCCAACTGAAACCC 58.010 50.000 5.01 0.00 0.00 4.11
1768 1780 5.940470 AGCAGAACGATAAACAGGAAGAAAT 59.060 36.000 0.00 0.00 0.00 2.17
1773 1785 5.185249 AGACTAGCAGAACGATAAACAGGAA 59.815 40.000 0.00 0.00 0.00 3.36
1782 1794 3.085533 ACAGTGAGACTAGCAGAACGAT 58.914 45.455 0.00 0.00 0.00 3.73
1802 1814 3.244457 ACTGGGTTGTTAGAGCTAACCAC 60.244 47.826 15.52 14.39 44.37 4.16
1825 1837 4.576463 GCCACTCCATAACTGAAATACTGG 59.424 45.833 0.00 0.00 0.00 4.00
1849 1861 2.552155 GGCAGGACACAACATAGGACAA 60.552 50.000 0.00 0.00 0.00 3.18
1918 1930 5.588958 AGAAGCAAATTTGGGCTATTCTC 57.411 39.130 19.47 6.16 40.01 2.87
1989 2003 1.169034 TGTGCACGCATGGCAGTAAA 61.169 50.000 13.13 0.00 42.85 2.01
2034 2049 5.007039 CAGTCACCTTGATCGGTATTGATTG 59.993 44.000 0.00 0.00 34.94 2.67
2049 2064 1.133513 TGTTGATTGGCCAGTCACCTT 60.134 47.619 28.84 0.00 0.00 3.50
2060 2075 5.740569 CACGATTCTAGCAAATGTTGATTGG 59.259 40.000 0.00 0.00 0.00 3.16
2125 2140 4.398988 GCATCATGTTCAGGTATTGGTCAA 59.601 41.667 0.00 0.00 0.00 3.18
2207 2222 3.129287 CACCCTGGTATGAGCAAAATCAC 59.871 47.826 0.00 0.00 30.46 3.06
2208 2223 3.355378 CACCCTGGTATGAGCAAAATCA 58.645 45.455 0.00 0.00 0.00 2.57
2209 2224 2.099756 GCACCCTGGTATGAGCAAAATC 59.900 50.000 0.00 0.00 0.00 2.17
2247 2262 6.893583 AGTTGTCATGGTCTATTAGCATTCT 58.106 36.000 0.00 0.00 43.83 2.40
2267 2282 3.632145 GGGCAGGTCCAATATACAAGTTG 59.368 47.826 0.00 0.00 36.21 3.16
2307 2322 5.469760 CAGAAAGATAGAGAGAGATCGAGCA 59.530 44.000 2.38 0.00 0.00 4.26
2312 2327 6.262944 TGACTGCAGAAAGATAGAGAGAGATC 59.737 42.308 23.35 1.12 0.00 2.75
2335 2350 3.833645 CCTCGAATCCGGCGGTGA 61.834 66.667 27.32 17.67 36.24 4.02
2381 2396 0.036952 CACCTCCTGCACGTCTGATT 60.037 55.000 0.00 0.00 0.00 2.57
2432 2447 0.820891 CTTGATGATCCTTGCCCCCG 60.821 60.000 0.00 0.00 0.00 5.73
2439 2454 2.683152 GCCTGCAGACTTGATGATCCTT 60.683 50.000 17.39 0.00 0.00 3.36
2440 2455 1.134159 GCCTGCAGACTTGATGATCCT 60.134 52.381 17.39 0.00 0.00 3.24
2622 2637 3.928375 GCATCGAAATTCACCTGCAAAAT 59.072 39.130 0.00 0.00 0.00 1.82
2667 2682 5.923733 TCCAGGAGAATCTTGTAGTTCTC 57.076 43.478 6.58 6.58 46.02 2.87
2722 2737 1.366319 AAGCCAGGAGAATCACCACT 58.634 50.000 0.00 0.00 36.25 4.00
2841 2857 0.321671 AGACTGAATCCCCACACACG 59.678 55.000 0.00 0.00 0.00 4.49
2857 2873 1.202371 TCACACACGACTGTTCCAGAC 60.202 52.381 0.00 0.00 35.18 3.51
2869 2885 3.876242 TGTTGACATCAATCACACACG 57.124 42.857 0.00 0.00 38.24 4.49
2952 2968 8.198109 AGTTTAGTACTATACACAGCAATGAGG 58.802 37.037 21.00 0.00 34.56 3.86
2996 3012 9.349713 ACTCTAATCTTAATGTTGTGTGGAAAA 57.650 29.630 0.00 0.00 0.00 2.29
3055 3071 1.970640 TCAGTTTGCTAGCTCACAGGA 59.029 47.619 17.23 10.80 0.00 3.86
3080 3096 0.460987 GGACAGAGATGAAGCACCCG 60.461 60.000 0.00 0.00 0.00 5.28
3203 3219 7.175990 ACGTCATAATCAGGGTTAAAACAACAT 59.824 33.333 0.00 0.00 0.00 2.71
3215 3231 5.723672 ATACTACCACGTCATAATCAGGG 57.276 43.478 0.00 0.00 0.00 4.45
3222 3238 6.602803 TGTCCACTTTATACTACCACGTCATA 59.397 38.462 0.00 0.00 0.00 2.15
3278 3294 3.541242 ACCAGGACATGATGGGAAAAA 57.459 42.857 16.84 0.00 41.13 1.94
3282 3298 2.241176 GGTAAACCAGGACATGATGGGA 59.759 50.000 16.84 3.75 41.13 4.37
3283 3299 2.654863 GGTAAACCAGGACATGATGGG 58.345 52.381 16.84 8.13 41.13 4.00
3284 3300 2.025416 TGGGTAAACCAGGACATGATGG 60.025 50.000 0.00 7.27 46.80 3.51
3367 3384 8.279103 GCAAGTATTAGCATAAAGTAGAGCTTG 58.721 37.037 0.00 0.00 37.52 4.01
3394 3411 8.020861 AGTATGCAATGCAAAATGTTACAAAG 57.979 30.769 13.45 0.00 43.62 2.77
3396 3413 7.871973 AGAAGTATGCAATGCAAAATGTTACAA 59.128 29.630 13.45 0.00 43.62 2.41
3412 3429 7.390823 TGTACTTGTCCATTTAGAAGTATGCA 58.609 34.615 0.00 0.00 37.50 3.96
3414 3431 8.338259 GCATGTACTTGTCCATTTAGAAGTATG 58.662 37.037 10.17 0.00 37.50 2.39
3453 3470 5.119931 AGATCTAGTCTGCATCATCGTTC 57.880 43.478 0.00 0.00 35.31 3.95
3465 3482 7.403671 TGGTTCTGTAGTTGTAGATCTAGTCT 58.596 38.462 1.64 4.81 41.11 3.24
3474 3491 5.812642 GTGATGGATGGTTCTGTAGTTGTAG 59.187 44.000 0.00 0.00 0.00 2.74
3476 3493 4.041567 TGTGATGGATGGTTCTGTAGTTGT 59.958 41.667 0.00 0.00 0.00 3.32
3482 3499 5.415701 GTGTTTATGTGATGGATGGTTCTGT 59.584 40.000 0.00 0.00 0.00 3.41
3501 3518 6.377146 ACAAGAACATACCTGACTTTGTGTTT 59.623 34.615 0.00 0.00 30.70 2.83
3548 3565 5.010314 TCAATCATAAGGCCATCAAGCATTC 59.990 40.000 5.01 0.00 37.93 2.67
3549 3566 4.897076 TCAATCATAAGGCCATCAAGCATT 59.103 37.500 5.01 0.00 40.38 3.56
3568 3585 5.591067 TGTGTCACATGATACATGCATCAAT 59.409 36.000 12.58 1.86 40.46 2.57
3590 3607 7.750229 AATTCAGATTTACTCATGTGTGTGT 57.250 32.000 10.62 0.00 36.20 3.72


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

AutoCloner maintained by Alex Coulton.