Multiple sequence alignment - TraesCS7D01G350200

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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 TraesCS7D01G350200 chr7D 100.000 2657 0 0 1 2657 451042162 451039506 0.000000e+00 4907.0
1 TraesCS7D01G350200 chr7D 89.187 1045 76 19 657 1681 449547710 449548737 0.000000e+00 1269.0
2 TraesCS7D01G350200 chr7D 78.286 175 31 6 2218 2386 557383598 557383425 3.620000e-19 106.0
3 TraesCS7D01G350200 chr7D 85.870 92 10 3 1712 1801 565299478 565299388 7.830000e-16 95.3
4 TraesCS7D01G350200 chr7D 83.696 92 13 2 1712 1801 565304309 565304218 4.710000e-13 86.1
5 TraesCS7D01G350200 chr7D 78.512 121 19 7 2231 2349 31380867 31380982 3.670000e-09 73.1
6 TraesCS7D01G350200 chr7D 80.723 83 11 4 336 415 616007103 616007023 2.860000e-05 60.2
7 TraesCS7D01G350200 chr7A 89.212 1548 121 28 199 1734 546045380 546046893 0.000000e+00 1892.0
8 TraesCS7D01G350200 chr7A 90.725 938 69 10 737 1670 546344114 546343191 0.000000e+00 1234.0
9 TraesCS7D01G350200 chr7A 87.500 160 15 2 1 160 546024801 546024955 2.100000e-41 180.0
10 TraesCS7D01G350200 chr7B 92.959 1264 72 7 608 1858 468828363 468827104 0.000000e+00 1825.0
11 TraesCS7D01G350200 chr7B 92.177 882 59 6 781 1659 472784808 472783934 0.000000e+00 1238.0
12 TraesCS7D01G350200 chr7B 93.151 730 45 4 953 1681 468051029 468051754 0.000000e+00 1066.0
13 TraesCS7D01G350200 chr7B 84.876 767 73 24 1904 2657 468825321 468824585 0.000000e+00 734.0
14 TraesCS7D01G350200 chr7B 95.167 269 11 1 1 267 468848981 468848713 8.790000e-115 424.0
15 TraesCS7D01G350200 chr7B 83.962 212 21 9 737 937 468050686 468050895 9.710000e-45 191.0
16 TraesCS7D01G350200 chr7B 82.051 78 14 0 488 565 339021340 339021263 1.710000e-07 67.6
17 TraesCS7D01G350200 chr7B 100.000 31 0 0 922 952 468050920 468050950 1.030000e-04 58.4
18 TraesCS7D01G350200 chr2A 80.591 237 44 2 330 565 602696185 602696420 5.840000e-42 182.0
19 TraesCS7D01G350200 chr2A 80.165 242 44 3 325 565 183333185 183332947 7.560000e-41 178.0
20 TraesCS7D01G350200 chr2A 86.813 91 9 2 1714 1801 758366471 758366561 6.050000e-17 99.0
21 TraesCS7D01G350200 chr2A 94.231 52 3 0 2552 2603 619609493 619609544 2.190000e-11 80.5
22 TraesCS7D01G350200 chr6D 81.223 229 38 5 332 556 129523356 129523583 2.100000e-41 180.0
23 TraesCS7D01G350200 chr6D 93.023 86 6 0 1150 1235 157662038 157662123 2.780000e-25 126.0
24 TraesCS7D01G350200 chr6D 82.353 119 16 5 2234 2349 4626589 4626705 6.050000e-17 99.0
25 TraesCS7D01G350200 chr2B 90.517 116 10 1 381 496 553634517 553634631 4.580000e-33 152.0
26 TraesCS7D01G350200 chr2B 92.157 51 2 2 2553 2601 193473068 193473018 1.320000e-08 71.3
27 TraesCS7D01G350200 chr5D 78.723 235 42 7 334 565 49301882 49301653 1.650000e-32 150.0
28 TraesCS7D01G350200 chr5D 89.286 84 8 1 1712 1794 371468128 371468045 1.300000e-18 104.0
29 TraesCS7D01G350200 chr5D 86.047 86 11 1 481 565 493132918 493132833 1.010000e-14 91.6
30 TraesCS7D01G350200 chr5D 95.556 45 2 0 2557 2601 515276021 515276065 3.670000e-09 73.1
31 TraesCS7D01G350200 chr4A 79.130 230 36 7 336 564 500655840 500655622 5.930000e-32 148.0
32 TraesCS7D01G350200 chr1D 85.484 124 15 3 2219 2342 444332121 444332241 2.780000e-25 126.0
33 TraesCS7D01G350200 chr1D 79.688 128 17 8 2207 2329 140052595 140052718 1.690000e-12 84.2
34 TraesCS7D01G350200 chr1D 93.750 48 3 0 2557 2604 462332937 462332890 3.670000e-09 73.1
35 TraesCS7D01G350200 chr1D 81.522 92 12 4 1715 1802 401562776 401562686 1.320000e-08 71.3
36 TraesCS7D01G350200 chr3D 94.737 76 4 0 1160 1235 105196646 105196571 4.650000e-23 119.0
37 TraesCS7D01G350200 chr3D 90.789 76 7 0 1160 1235 105252410 105252335 4.680000e-18 102.0
38 TraesCS7D01G350200 chr3D 88.158 76 8 1 2258 2333 109069562 109069488 3.640000e-14 89.8
39 TraesCS7D01G350200 chr2D 89.474 76 7 1 1712 1786 605620909 605620834 7.830000e-16 95.3
40 TraesCS7D01G350200 chr6A 80.342 117 19 4 2233 2346 186860511 186860626 4.710000e-13 86.1
41 TraesCS7D01G350200 chr5A 79.389 131 20 7 2216 2341 661218168 661218040 4.710000e-13 86.1
42 TraesCS7D01G350200 chr5A 91.111 45 4 0 2555 2599 123308383 123308339 7.940000e-06 62.1
43 TraesCS7D01G350200 chr1A 94.340 53 3 0 2552 2604 575655622 575655570 6.100000e-12 82.4
44 TraesCS7D01G350200 chr6B 79.832 119 15 9 2232 2344 257990628 257990513 7.890000e-11 78.7
45 TraesCS7D01G350200 chr3B 82.292 96 6 6 2557 2644 193404607 193404699 3.670000e-09 73.1
46 TraesCS7D01G350200 chr1B 93.750 48 3 0 2557 2604 637395490 637395443 3.670000e-09 73.1
47 TraesCS7D01G350200 chr4D 81.818 88 12 4 1713 1797 502049603 502049517 1.320000e-08 71.3
48 TraesCS7D01G350200 chr4D 90.000 50 4 1 2552 2601 459315742 459315790 2.210000e-06 63.9
49 TraesCS7D01G350200 chr3A 88.462 52 4 2 2478 2528 575884292 575884242 7.940000e-06 62.1


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 TraesCS7D01G350200 chr7D 451039506 451042162 2656 True 4907.000000 4907 100.0000 1 2657 1 chr7D.!!$R1 2656
1 TraesCS7D01G350200 chr7D 449547710 449548737 1027 False 1269.000000 1269 89.1870 657 1681 1 chr7D.!!$F2 1024
2 TraesCS7D01G350200 chr7A 546045380 546046893 1513 False 1892.000000 1892 89.2120 199 1734 1 chr7A.!!$F2 1535
3 TraesCS7D01G350200 chr7A 546343191 546344114 923 True 1234.000000 1234 90.7250 737 1670 1 chr7A.!!$R1 933
4 TraesCS7D01G350200 chr7B 468824585 468828363 3778 True 1279.500000 1825 88.9175 608 2657 2 chr7B.!!$R4 2049
5 TraesCS7D01G350200 chr7B 472783934 472784808 874 True 1238.000000 1238 92.1770 781 1659 1 chr7B.!!$R3 878
6 TraesCS7D01G350200 chr7B 468050686 468051754 1068 False 438.466667 1066 92.3710 737 1681 3 chr7B.!!$F1 944

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
323 324 0.033796 ATGCCACAGGGAATGGACTG 60.034 55.0 0.0 0.0 39.87 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 4188 0.586319 CGTGCCTCAGCGAAAGAAAA 59.414 50.0 0.0 0.0 44.31 2.29 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
52 53 9.160576 TCAGAAATAACATTTAAAACGTTGACG 57.839 29.630 0.00 1.41 46.33 4.35
64 65 2.706760 CGTTGACGTCGTTGTTTCTT 57.293 45.000 11.62 0.00 34.11 2.52
65 66 3.029167 CGTTGACGTCGTTGTTTCTTT 57.971 42.857 11.62 0.00 34.11 2.52
66 67 3.409949 CGTTGACGTCGTTGTTTCTTTT 58.590 40.909 11.62 0.00 34.11 2.27
67 68 3.472495 CGTTGACGTCGTTGTTTCTTTTC 59.528 43.478 11.62 0.00 34.11 2.29
68 69 4.396519 GTTGACGTCGTTGTTTCTTTTCA 58.603 39.130 11.62 0.00 0.00 2.69
69 70 4.868450 TGACGTCGTTGTTTCTTTTCAT 57.132 36.364 11.62 0.00 0.00 2.57
70 71 4.828704 TGACGTCGTTGTTTCTTTTCATC 58.171 39.130 11.62 0.00 0.00 2.92
71 72 4.205323 ACGTCGTTGTTTCTTTTCATCC 57.795 40.909 0.00 0.00 0.00 3.51
72 73 3.002965 ACGTCGTTGTTTCTTTTCATCCC 59.997 43.478 0.00 0.00 0.00 3.85
73 74 3.250040 CGTCGTTGTTTCTTTTCATCCCT 59.750 43.478 0.00 0.00 0.00 4.20
74 75 4.610680 CGTCGTTGTTTCTTTTCATCCCTC 60.611 45.833 0.00 0.00 0.00 4.30
75 76 3.818773 TCGTTGTTTCTTTTCATCCCTCC 59.181 43.478 0.00 0.00 0.00 4.30
76 77 3.568007 CGTTGTTTCTTTTCATCCCTCCA 59.432 43.478 0.00 0.00 0.00 3.86
77 78 4.218417 CGTTGTTTCTTTTCATCCCTCCAT 59.782 41.667 0.00 0.00 0.00 3.41
78 79 5.278957 CGTTGTTTCTTTTCATCCCTCCATT 60.279 40.000 0.00 0.00 0.00 3.16
79 80 5.982890 TGTTTCTTTTCATCCCTCCATTC 57.017 39.130 0.00 0.00 0.00 2.67
80 81 5.392995 TGTTTCTTTTCATCCCTCCATTCA 58.607 37.500 0.00 0.00 0.00 2.57
81 82 6.018469 TGTTTCTTTTCATCCCTCCATTCAT 58.982 36.000 0.00 0.00 0.00 2.57
82 83 6.071221 TGTTTCTTTTCATCCCTCCATTCATG 60.071 38.462 0.00 0.00 0.00 3.07
83 84 5.197224 TCTTTTCATCCCTCCATTCATGT 57.803 39.130 0.00 0.00 0.00 3.21
84 85 5.582953 TCTTTTCATCCCTCCATTCATGTT 58.417 37.500 0.00 0.00 0.00 2.71
85 86 5.419788 TCTTTTCATCCCTCCATTCATGTTG 59.580 40.000 0.00 0.00 0.00 3.33
86 87 4.320546 TTCATCCCTCCATTCATGTTGT 57.679 40.909 0.00 0.00 0.00 3.32
87 88 3.623703 TCATCCCTCCATTCATGTTGTG 58.376 45.455 0.00 0.00 0.00 3.33
88 89 2.512692 TCCCTCCATTCATGTTGTGG 57.487 50.000 7.24 7.24 0.00 4.17
89 90 1.710244 TCCCTCCATTCATGTTGTGGT 59.290 47.619 11.57 0.00 34.61 4.16
90 91 1.820519 CCCTCCATTCATGTTGTGGTG 59.179 52.381 11.57 9.76 34.61 4.17
91 92 1.203052 CCTCCATTCATGTTGTGGTGC 59.797 52.381 11.57 0.00 34.61 5.01
92 93 2.165167 CTCCATTCATGTTGTGGTGCT 58.835 47.619 11.57 0.00 34.61 4.40
93 94 3.346315 CTCCATTCATGTTGTGGTGCTA 58.654 45.455 11.57 0.00 34.61 3.49
94 95 3.949754 CTCCATTCATGTTGTGGTGCTAT 59.050 43.478 11.57 0.00 34.61 2.97
95 96 5.109500 TCCATTCATGTTGTGGTGCTATA 57.891 39.130 11.57 0.00 34.61 1.31
96 97 5.693961 TCCATTCATGTTGTGGTGCTATAT 58.306 37.500 11.57 0.00 34.61 0.86
97 98 6.128486 TCCATTCATGTTGTGGTGCTATATT 58.872 36.000 11.57 0.00 34.61 1.28
98 99 6.039605 TCCATTCATGTTGTGGTGCTATATTG 59.960 38.462 11.57 0.00 34.61 1.90
99 100 4.898829 TCATGTTGTGGTGCTATATTGC 57.101 40.909 1.87 1.87 0.00 3.56
100 101 4.525996 TCATGTTGTGGTGCTATATTGCT 58.474 39.130 10.48 0.00 0.00 3.91
101 102 5.679601 TCATGTTGTGGTGCTATATTGCTA 58.320 37.500 10.48 0.00 0.00 3.49
102 103 5.759763 TCATGTTGTGGTGCTATATTGCTAG 59.240 40.000 10.48 0.00 0.00 3.42
103 104 3.876914 TGTTGTGGTGCTATATTGCTAGC 59.123 43.478 8.10 8.10 43.61 3.42
104 105 2.754472 TGTGGTGCTATATTGCTAGCG 58.246 47.619 10.77 0.00 45.78 4.26
107 108 0.093705 GTGCTATATTGCTAGCGCGC 59.906 55.000 26.66 26.66 45.78 6.86
108 109 1.014044 TGCTATATTGCTAGCGCGCC 61.014 55.000 30.33 13.83 45.78 6.53
109 110 1.991430 CTATATTGCTAGCGCGCCG 59.009 57.895 30.33 20.75 39.65 6.46
110 111 0.456142 CTATATTGCTAGCGCGCCGA 60.456 55.000 30.33 15.98 39.65 5.54
111 112 0.038983 TATATTGCTAGCGCGCCGAA 60.039 50.000 30.33 15.69 39.65 4.30
112 113 1.284982 ATATTGCTAGCGCGCCGAAG 61.285 55.000 30.33 23.26 39.65 3.79
116 117 2.354656 CTAGCGCGCCGAAGCATA 60.355 61.111 30.33 10.85 39.83 3.14
117 118 1.734477 CTAGCGCGCCGAAGCATAT 60.734 57.895 30.33 8.40 39.83 1.78
118 119 1.949015 CTAGCGCGCCGAAGCATATG 61.949 60.000 30.33 0.00 39.83 1.78
119 120 2.693250 TAGCGCGCCGAAGCATATGT 62.693 55.000 30.33 6.92 39.83 2.29
120 121 2.246397 CGCGCCGAAGCATATGTG 59.754 61.111 0.00 0.00 39.83 3.21
121 122 2.525248 CGCGCCGAAGCATATGTGT 61.525 57.895 0.00 0.00 39.83 3.72
122 123 1.721487 GCGCCGAAGCATATGTGTT 59.279 52.632 4.29 0.00 39.83 3.32
123 124 0.098728 GCGCCGAAGCATATGTGTTT 59.901 50.000 4.29 0.00 39.83 2.83
124 125 1.329292 GCGCCGAAGCATATGTGTTTA 59.671 47.619 4.29 0.00 39.83 2.01
125 126 2.032030 GCGCCGAAGCATATGTGTTTAT 60.032 45.455 4.29 0.00 39.83 1.40
126 127 3.548014 GCGCCGAAGCATATGTGTTTATT 60.548 43.478 4.29 0.00 39.83 1.40
127 128 4.211389 CGCCGAAGCATATGTGTTTATTC 58.789 43.478 4.29 0.00 39.83 1.75
128 129 4.537015 GCCGAAGCATATGTGTTTATTCC 58.463 43.478 4.29 0.00 39.53 3.01
129 130 4.036262 GCCGAAGCATATGTGTTTATTCCA 59.964 41.667 4.29 0.00 39.53 3.53
130 131 5.278463 GCCGAAGCATATGTGTTTATTCCAT 60.278 40.000 4.29 0.00 39.53 3.41
131 132 6.373779 CCGAAGCATATGTGTTTATTCCATC 58.626 40.000 4.29 0.00 0.00 3.51
132 133 6.205464 CCGAAGCATATGTGTTTATTCCATCT 59.795 38.462 4.29 0.00 0.00 2.90
133 134 7.255242 CCGAAGCATATGTGTTTATTCCATCTT 60.255 37.037 4.29 0.00 0.00 2.40
134 135 8.773645 CGAAGCATATGTGTTTATTCCATCTTA 58.226 33.333 4.29 0.00 0.00 2.10
135 136 9.884465 GAAGCATATGTGTTTATTCCATCTTAC 57.116 33.333 4.29 0.00 0.00 2.34
136 137 9.632638 AAGCATATGTGTTTATTCCATCTTACT 57.367 29.630 4.29 0.00 0.00 2.24
137 138 9.632638 AGCATATGTGTTTATTCCATCTTACTT 57.367 29.630 4.29 0.00 0.00 2.24
138 139 9.669353 GCATATGTGTTTATTCCATCTTACTTG 57.331 33.333 4.29 0.00 0.00 3.16
143 144 9.513906 TGTGTTTATTCCATCTTACTTGATTGA 57.486 29.630 0.00 0.00 0.00 2.57
174 175 7.150783 AGATAGCTGTTTCAGAACAAATTCC 57.849 36.000 0.00 0.00 44.65 3.01
175 176 6.716628 AGATAGCTGTTTCAGAACAAATTCCA 59.283 34.615 0.00 0.00 44.65 3.53
176 177 5.796424 AGCTGTTTCAGAACAAATTCCAT 57.204 34.783 0.66 0.00 44.65 3.41
177 178 5.776744 AGCTGTTTCAGAACAAATTCCATC 58.223 37.500 0.66 0.00 44.65 3.51
178 179 5.537674 AGCTGTTTCAGAACAAATTCCATCT 59.462 36.000 0.66 0.00 44.65 2.90
179 180 6.041296 AGCTGTTTCAGAACAAATTCCATCTT 59.959 34.615 0.66 0.00 44.65 2.40
180 181 7.231317 AGCTGTTTCAGAACAAATTCCATCTTA 59.769 33.333 0.66 0.00 44.65 2.10
181 182 7.327032 GCTGTTTCAGAACAAATTCCATCTTAC 59.673 37.037 0.66 0.00 44.65 2.34
182 183 8.463930 TGTTTCAGAACAAATTCCATCTTACT 57.536 30.769 0.00 0.00 42.54 2.24
183 184 8.912988 TGTTTCAGAACAAATTCCATCTTACTT 58.087 29.630 0.00 0.00 42.54 2.24
184 185 9.185192 GTTTCAGAACAAATTCCATCTTACTTG 57.815 33.333 0.00 0.00 35.18 3.16
185 186 8.690203 TTCAGAACAAATTCCATCTTACTTGA 57.310 30.769 0.00 0.00 35.18 3.02
186 187 8.868522 TCAGAACAAATTCCATCTTACTTGAT 57.131 30.769 0.00 0.00 35.18 2.57
187 188 9.300681 TCAGAACAAATTCCATCTTACTTGATT 57.699 29.630 0.00 0.00 35.18 2.57
188 189 9.350357 CAGAACAAATTCCATCTTACTTGATTG 57.650 33.333 0.00 0.00 35.18 2.67
189 190 9.300681 AGAACAAATTCCATCTTACTTGATTGA 57.699 29.630 0.00 0.00 35.18 2.57
190 191 9.912634 GAACAAATTCCATCTTACTTGATTGAA 57.087 29.630 0.00 0.00 34.23 2.69
229 230 8.600625 GTTTCAAAACAAAACCCATCTTACTTC 58.399 33.333 0.81 0.00 38.74 3.01
234 235 7.595819 AACAAAACCCATCTTACTTCATTGA 57.404 32.000 0.00 0.00 0.00 2.57
282 283 6.074356 ACAAATATCTTGCTTTGCGAAAACAC 60.074 34.615 0.00 0.00 36.12 3.32
312 313 6.638096 TTTCATACATATTGGATGCCACAG 57.362 37.500 0.00 0.00 38.58 3.66
313 314 4.654915 TCATACATATTGGATGCCACAGG 58.345 43.478 0.00 0.00 38.58 4.00
318 319 1.784358 ATTGGATGCCACAGGGAATG 58.216 50.000 0.00 0.00 29.90 2.67
323 324 0.033796 ATGCCACAGGGAATGGACTG 60.034 55.000 0.00 0.00 39.87 3.51
327 328 2.885554 GCCACAGGGAATGGACTGAAAT 60.886 50.000 0.00 0.00 39.87 2.17
355 356 5.741011 ACCCAAATGATAAGTGTCATACGT 58.259 37.500 0.00 0.00 37.85 3.57
356 357 5.584649 ACCCAAATGATAAGTGTCATACGTG 59.415 40.000 0.00 0.00 37.85 4.49
357 358 5.584649 CCCAAATGATAAGTGTCATACGTGT 59.415 40.000 0.00 0.00 37.85 4.49
359 360 7.042725 CCCAAATGATAAGTGTCATACGTGTAG 60.043 40.741 0.00 0.00 37.85 2.74
376 377 2.355837 GCACGAAGCACTCCGTCA 60.356 61.111 0.00 0.00 44.79 4.35
377 378 1.738099 GCACGAAGCACTCCGTCAT 60.738 57.895 0.00 0.00 44.79 3.06
379 380 1.990799 CACGAAGCACTCCGTCATTA 58.009 50.000 0.00 0.00 36.83 1.90
380 381 2.333926 CACGAAGCACTCCGTCATTAA 58.666 47.619 0.00 0.00 36.83 1.40
381 382 2.930040 CACGAAGCACTCCGTCATTAAT 59.070 45.455 0.00 0.00 36.83 1.40
424 425 7.071014 TGCCATTTGAAAAGAGAAAACAAAC 57.929 32.000 0.00 0.00 34.21 2.93
425 426 6.093357 TGCCATTTGAAAAGAGAAAACAAACC 59.907 34.615 0.00 0.00 34.21 3.27
426 427 6.458206 GCCATTTGAAAAGAGAAAACAAACCC 60.458 38.462 0.00 0.00 34.21 4.11
445 446 3.177997 CCCCCAAAACACTGAAACTTG 57.822 47.619 0.00 0.00 0.00 3.16
451 452 4.270808 CCAAAACACTGAAACTTGCCATTC 59.729 41.667 0.00 0.00 0.00 2.67
452 453 4.734398 AAACACTGAAACTTGCCATTCA 57.266 36.364 0.00 0.00 34.57 2.57
457 459 5.351189 ACACTGAAACTTGCCATTCAAAAAC 59.649 36.000 0.00 0.00 35.31 2.43
465 467 5.704978 ACTTGCCATTCAAAAACAAAGTTGT 59.295 32.000 0.00 0.00 37.32 3.32
499 501 7.875971 ACAACTAAAATTGTCATCCTCACTTC 58.124 34.615 0.00 0.00 38.44 3.01
508 510 6.174720 TGTCATCCTCACTTCACTAAACTT 57.825 37.500 0.00 0.00 0.00 2.66
510 512 5.992217 GTCATCCTCACTTCACTAAACTTGT 59.008 40.000 0.00 0.00 0.00 3.16
511 513 6.146347 GTCATCCTCACTTCACTAAACTTGTC 59.854 42.308 0.00 0.00 0.00 3.18
512 514 5.607939 TCCTCACTTCACTAAACTTGTCA 57.392 39.130 0.00 0.00 0.00 3.58
513 515 6.174720 TCCTCACTTCACTAAACTTGTCAT 57.825 37.500 0.00 0.00 0.00 3.06
531 533 8.257306 ACTTGTCATAAAAATGTTTGGAGTTGT 58.743 29.630 0.00 0.00 0.00 3.32
535 537 9.906660 GTCATAAAAATGTTTGGAGTTGTCATA 57.093 29.630 0.00 0.00 0.00 2.15
541 543 9.787532 AAAATGTTTGGAGTTGTCATATATTCG 57.212 29.630 0.00 0.00 0.00 3.34
542 544 8.506168 AATGTTTGGAGTTGTCATATATTCGT 57.494 30.769 0.00 0.00 0.00 3.85
543 545 9.607988 AATGTTTGGAGTTGTCATATATTCGTA 57.392 29.630 0.00 0.00 0.00 3.43
544 546 8.642908 TGTTTGGAGTTGTCATATATTCGTAG 57.357 34.615 0.00 0.00 0.00 3.51
545 547 7.223971 TGTTTGGAGTTGTCATATATTCGTAGC 59.776 37.037 0.00 0.00 0.00 3.58
546 548 6.399639 TGGAGTTGTCATATATTCGTAGCA 57.600 37.500 0.00 0.00 0.00 3.49
547 549 6.213677 TGGAGTTGTCATATATTCGTAGCAC 58.786 40.000 0.00 0.00 0.00 4.40
548 550 6.183360 TGGAGTTGTCATATATTCGTAGCACA 60.183 38.462 0.00 0.00 0.00 4.57
549 551 6.144080 GGAGTTGTCATATATTCGTAGCACAC 59.856 42.308 0.00 0.00 0.00 3.82
568 570 4.986034 CACACGTGTGGTTCTTATCAAGTA 59.014 41.667 35.65 0.00 42.10 2.24
570 572 6.147164 CACACGTGTGGTTCTTATCAAGTAAT 59.853 38.462 35.65 0.00 42.10 1.89
581 583 6.650120 TCTTATCAAGTAATCAGGGTCCAAC 58.350 40.000 0.00 0.00 0.00 3.77
584 586 4.651778 TCAAGTAATCAGGGTCCAACTTG 58.348 43.478 6.67 6.67 43.15 3.16
585 587 4.349636 TCAAGTAATCAGGGTCCAACTTGA 59.650 41.667 10.70 10.70 46.24 3.02
597 599 5.925969 GGGTCCAACTTGAAAAACATGTATG 59.074 40.000 0.00 0.00 36.16 2.39
691 701 3.069016 ACACCAGAGTCAACACGTCAATA 59.931 43.478 0.00 0.00 0.00 1.90
727 737 1.317431 TATGCTGCCGTACGTGAGGT 61.317 55.000 15.21 0.00 0.00 3.85
751 778 5.010282 AGCCAGTAACCAAGTAAGAAATGG 58.990 41.667 0.00 0.00 40.16 3.16
856 892 2.311124 AAATCCTTAAGCCGACCGAG 57.689 50.000 0.00 0.00 0.00 4.63
862 898 0.171903 TTAAGCCGACCGAGCACTAC 59.828 55.000 5.87 0.00 0.00 2.73
905 954 1.078356 CAGCACTGCATCCTCAGCT 60.078 57.895 3.30 0.00 37.59 4.24
906 955 1.090625 CAGCACTGCATCCTCAGCTC 61.091 60.000 3.30 0.00 37.59 4.09
907 956 1.078637 GCACTGCATCCTCAGCTCA 60.079 57.895 0.00 0.00 37.59 4.26
908 957 0.464013 GCACTGCATCCTCAGCTCAT 60.464 55.000 0.00 0.00 37.59 2.90
918 967 1.134159 CCTCAGCTCATTCCTTCCTGG 60.134 57.143 0.00 0.00 37.10 4.45
983 1150 4.395231 TGATTACACACTCTGGTCTCTACG 59.605 45.833 0.00 0.00 0.00 3.51
1092 1264 1.136147 CGACGTCTTCAGGTACCGG 59.864 63.158 14.70 5.86 0.00 5.28
1251 1423 2.044053 ACATCATGGGTTGGCCGG 60.044 61.111 0.00 0.00 34.97 6.13
1380 1552 3.980989 TTCGCGTACGTGTGCCCT 61.981 61.111 26.44 0.00 41.18 5.19
1452 1624 2.765807 CCGGTCTGCCTGGAGGAT 60.766 66.667 0.00 0.00 37.39 3.24
1467 1639 2.028484 GATATCCACGGCGGCGAA 59.972 61.111 38.93 22.08 33.14 4.70
1632 1807 4.500116 GAGGCGCCTCAGTCGTCC 62.500 72.222 44.10 20.82 42.31 4.79
1663 1838 4.405036 TGTTGCCACCGGTGTAGTTATATA 59.595 41.667 31.80 7.33 0.00 0.86
1745 1920 7.712264 TGTAAGTTGCCTGAAAATTGAATTG 57.288 32.000 0.00 0.00 0.00 2.32
1747 1922 4.644498 AGTTGCCTGAAAATTGAATTGGG 58.356 39.130 0.00 0.00 0.00 4.12
1748 1923 4.102996 AGTTGCCTGAAAATTGAATTGGGT 59.897 37.500 0.00 0.00 0.00 4.51
1749 1924 4.270245 TGCCTGAAAATTGAATTGGGTC 57.730 40.909 0.00 0.00 0.00 4.46
1750 1925 3.645212 TGCCTGAAAATTGAATTGGGTCA 59.355 39.130 0.00 0.00 0.00 4.02
1751 1926 4.248058 GCCTGAAAATTGAATTGGGTCAG 58.752 43.478 14.66 14.66 0.00 3.51
1752 1927 4.262592 GCCTGAAAATTGAATTGGGTCAGT 60.263 41.667 17.77 0.00 30.51 3.41
1754 1929 5.119931 TGAAAATTGAATTGGGTCAGTCG 57.880 39.130 0.00 0.00 0.00 4.18
1777 1953 3.648339 TTTTCTGCCAGTTGATTGCTC 57.352 42.857 0.00 0.00 0.00 4.26
1786 1962 4.187694 CCAGTTGATTGCTCCTCTAAGAC 58.812 47.826 0.00 0.00 0.00 3.01
1827 2006 9.814899 CTCTTTCTTTCAGAATCTGCTATCTTA 57.185 33.333 5.18 0.00 33.67 2.10
1877 3823 8.635765 TTTAGGCTGAGAATTTGTGACTAATT 57.364 30.769 4.74 4.74 0.00 1.40
1918 3864 9.613428 TTTTTAGGTGTATCTCTACATTGGATG 57.387 33.333 0.00 0.00 39.93 3.51
1919 3865 8.547481 TTTAGGTGTATCTCTACATTGGATGA 57.453 34.615 0.00 0.00 39.93 2.92
1920 3866 8.547481 TTAGGTGTATCTCTACATTGGATGAA 57.453 34.615 0.00 0.00 39.93 2.57
1921 3867 7.623999 AGGTGTATCTCTACATTGGATGAAT 57.376 36.000 0.00 0.00 39.93 2.57
1922 3868 7.675062 AGGTGTATCTCTACATTGGATGAATC 58.325 38.462 0.00 0.00 39.93 2.52
1923 3869 7.512058 AGGTGTATCTCTACATTGGATGAATCT 59.488 37.037 0.00 0.00 39.93 2.40
1924 3870 7.601886 GGTGTATCTCTACATTGGATGAATCTG 59.398 40.741 0.00 0.00 39.93 2.90
1925 3871 7.117523 GTGTATCTCTACATTGGATGAATCTGC 59.882 40.741 0.00 0.00 39.93 4.26
1926 3872 5.883685 TCTCTACATTGGATGAATCTGCT 57.116 39.130 0.00 0.00 0.00 4.24
1927 3873 6.983906 TCTCTACATTGGATGAATCTGCTA 57.016 37.500 0.00 0.00 0.00 3.49
1928 3874 7.550597 TCTCTACATTGGATGAATCTGCTAT 57.449 36.000 0.00 0.00 0.00 2.97
1929 3875 7.609960 TCTCTACATTGGATGAATCTGCTATC 58.390 38.462 0.00 0.00 0.00 2.08
1930 3876 7.454066 TCTCTACATTGGATGAATCTGCTATCT 59.546 37.037 0.00 0.00 0.00 1.98
1931 3877 7.609960 TCTACATTGGATGAATCTGCTATCTC 58.390 38.462 0.00 0.00 0.00 2.75
1932 3878 6.436738 ACATTGGATGAATCTGCTATCTCT 57.563 37.500 0.00 0.00 0.00 3.10
1933 3879 7.550597 ACATTGGATGAATCTGCTATCTCTA 57.449 36.000 0.00 0.00 0.00 2.43
1934 3880 7.385267 ACATTGGATGAATCTGCTATCTCTAC 58.615 38.462 0.00 0.00 0.00 2.59
1937 3883 7.550597 TGGATGAATCTGCTATCTCTACATT 57.449 36.000 0.00 0.00 0.00 2.71
1942 3888 4.597404 TCTGCTATCTCTACATTGGCTG 57.403 45.455 0.00 0.00 0.00 4.85
2004 3950 2.691409 TCTGAAAACCCAGCTATCCG 57.309 50.000 0.00 0.00 34.28 4.18
2006 3952 1.209504 CTGAAAACCCAGCTATCCGGA 59.790 52.381 6.61 6.61 0.00 5.14
2040 3986 0.320697 AAGTACTCGTTGTGGGGCTC 59.679 55.000 0.00 0.00 0.00 4.70
2042 3988 2.288025 TACTCGTTGTGGGGCTCCC 61.288 63.158 0.00 0.72 45.71 4.30
2086 4032 2.223502 ACCGTCACATATCACGTGCTAG 60.224 50.000 11.67 3.09 34.06 3.42
2089 4035 1.754226 TCACATATCACGTGCTAGGCA 59.246 47.619 11.67 0.00 35.60 4.75
2098 4044 4.040645 TGCTAGGCACTCTCCCAG 57.959 61.111 0.00 0.00 41.75 4.45
2099 4045 1.388133 TGCTAGGCACTCTCCCAGA 59.612 57.895 0.00 0.00 41.75 3.86
2100 4046 0.252239 TGCTAGGCACTCTCCCAGAA 60.252 55.000 0.00 0.00 41.75 3.02
2101 4047 1.127343 GCTAGGCACTCTCCCAGAAT 58.873 55.000 0.00 0.00 41.75 2.40
2102 4048 1.488393 GCTAGGCACTCTCCCAGAATT 59.512 52.381 0.00 0.00 41.75 2.17
2103 4049 2.092699 GCTAGGCACTCTCCCAGAATTT 60.093 50.000 0.00 0.00 41.75 1.82
2104 4050 2.797177 AGGCACTCTCCCAGAATTTC 57.203 50.000 0.00 0.00 0.00 2.17
2105 4051 1.283321 AGGCACTCTCCCAGAATTTCC 59.717 52.381 0.00 0.00 0.00 3.13
2189 4141 3.691698 TTGGTTGGTTTCCCTAGGTTT 57.308 42.857 8.29 0.00 0.00 3.27
2190 4142 3.691698 TGGTTGGTTTCCCTAGGTTTT 57.308 42.857 8.29 0.00 0.00 2.43
2254 4206 2.774439 TTTTTCTTTCGCTGAGGCAC 57.226 45.000 0.00 0.00 38.60 5.01
2279 4231 0.888619 TAGTTCTCGTGGAGGCACAG 59.111 55.000 0.00 0.00 0.00 3.66
2321 4273 4.910956 CGTGCCTCTCGGAAATGA 57.089 55.556 0.00 0.00 0.00 2.57
2325 4277 2.699954 GTGCCTCTCGGAAATGAGAAA 58.300 47.619 0.00 0.00 44.03 2.52
2372 4327 1.001860 GGAGCCATAGATGTGCCTCTC 59.998 57.143 0.00 0.00 0.00 3.20
2374 4329 0.320247 GCCATAGATGTGCCTCTCGG 60.320 60.000 0.00 0.00 0.00 4.63
2375 4330 1.332195 CCATAGATGTGCCTCTCGGA 58.668 55.000 0.00 0.00 0.00 4.55
2376 4331 1.688735 CCATAGATGTGCCTCTCGGAA 59.311 52.381 0.00 0.00 0.00 4.30
2377 4332 2.103094 CCATAGATGTGCCTCTCGGAAA 59.897 50.000 0.00 0.00 0.00 3.13
2378 4333 3.388308 CATAGATGTGCCTCTCGGAAAG 58.612 50.000 0.00 0.00 0.00 2.62
2379 4334 1.561643 AGATGTGCCTCTCGGAAAGA 58.438 50.000 0.00 0.00 0.00 2.52
2380 4335 1.902508 AGATGTGCCTCTCGGAAAGAA 59.097 47.619 0.00 0.00 32.23 2.52
2408 4363 4.176271 AGCTCATTTTATTTTGCTTCCGC 58.824 39.130 0.00 0.00 0.00 5.54
2409 4364 3.925913 GCTCATTTTATTTTGCTTCCGCA 59.074 39.130 0.00 0.00 46.24 5.69
2426 4381 2.609350 CGCAAGGCACATATTTGCTTT 58.391 42.857 13.29 9.41 42.12 3.51
2433 4388 3.429085 GCACATATTTGCTTTCGTGAGG 58.571 45.455 6.60 0.00 39.59 3.86
2451 4406 1.494721 AGGTGTGCCTCTTGGAAAAGA 59.505 47.619 0.00 0.00 42.67 2.52
2452 4407 2.091885 AGGTGTGCCTCTTGGAAAAGAA 60.092 45.455 0.00 0.00 42.67 2.52
2497 4452 9.778741 AAGAGACACATATTTACTTCTTGTGAA 57.221 29.630 8.22 0.00 39.98 3.18
2540 4495 7.218583 TCGAAAAAGTAAAATGACACGTTTTCC 59.781 33.333 15.28 0.00 43.78 3.13
2542 4497 8.535690 AAAAAGTAAAATGACACGTTTTCCAA 57.464 26.923 5.20 0.00 33.12 3.53
2543 4498 8.535690 AAAAGTAAAATGACACGTTTTCCAAA 57.464 26.923 5.20 0.00 31.71 3.28
2544 4499 8.535690 AAAGTAAAATGACACGTTTTCCAAAA 57.464 26.923 5.20 0.00 31.71 2.44
2545 4500 8.535690 AAGTAAAATGACACGTTTTCCAAAAA 57.464 26.923 5.20 0.00 31.71 1.94
2586 4541 3.185797 ACAAATTTACTTCTCGTGGACGC 59.814 43.478 0.00 0.00 39.60 5.19
2601 4556 0.874390 GACGCACAGATTTGCTTCCA 59.126 50.000 0.00 0.00 40.62 3.53
2652 4607 8.873830 GTTTTCTTTTTCTTTTTCCTTGAGAGG 58.126 33.333 0.00 0.00 45.02 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.160576 CGTCAACGTTTTAAATGTTATTTCTGA 57.839 29.630 13.97 5.57 38.51 3.27
45 46 2.706760 AAGAAACAACGACGTCAACG 57.293 45.000 17.16 4.83 46.33 4.10
46 47 4.396519 TGAAAAGAAACAACGACGTCAAC 58.603 39.130 17.16 0.00 0.00 3.18
47 48 4.665281 TGAAAAGAAACAACGACGTCAA 57.335 36.364 17.16 0.00 0.00 3.18
48 49 4.260456 GGATGAAAAGAAACAACGACGTCA 60.260 41.667 17.16 0.00 0.00 4.35
49 50 4.209112 GGATGAAAAGAAACAACGACGTC 58.791 43.478 5.18 5.18 0.00 4.34
50 51 3.002965 GGGATGAAAAGAAACAACGACGT 59.997 43.478 0.00 0.00 0.00 4.34
51 52 3.250040 AGGGATGAAAAGAAACAACGACG 59.750 43.478 0.00 0.00 0.00 5.12
52 53 4.320275 GGAGGGATGAAAAGAAACAACGAC 60.320 45.833 0.00 0.00 0.00 4.34
53 54 3.818773 GGAGGGATGAAAAGAAACAACGA 59.181 43.478 0.00 0.00 0.00 3.85
54 55 3.568007 TGGAGGGATGAAAAGAAACAACG 59.432 43.478 0.00 0.00 0.00 4.10
55 56 5.728637 ATGGAGGGATGAAAAGAAACAAC 57.271 39.130 0.00 0.00 0.00 3.32
56 57 5.837979 TGAATGGAGGGATGAAAAGAAACAA 59.162 36.000 0.00 0.00 0.00 2.83
57 58 5.392995 TGAATGGAGGGATGAAAAGAAACA 58.607 37.500 0.00 0.00 0.00 2.83
58 59 5.982890 TGAATGGAGGGATGAAAAGAAAC 57.017 39.130 0.00 0.00 0.00 2.78
59 60 6.018469 ACATGAATGGAGGGATGAAAAGAAA 58.982 36.000 0.00 0.00 0.00 2.52
60 61 5.582953 ACATGAATGGAGGGATGAAAAGAA 58.417 37.500 0.00 0.00 0.00 2.52
61 62 5.197224 ACATGAATGGAGGGATGAAAAGA 57.803 39.130 0.00 0.00 0.00 2.52
62 63 5.186409 ACAACATGAATGGAGGGATGAAAAG 59.814 40.000 0.00 0.00 0.00 2.27
63 64 5.047164 CACAACATGAATGGAGGGATGAAAA 60.047 40.000 0.00 0.00 0.00 2.29
64 65 4.463539 CACAACATGAATGGAGGGATGAAA 59.536 41.667 0.00 0.00 0.00 2.69
65 66 4.018490 CACAACATGAATGGAGGGATGAA 58.982 43.478 0.00 0.00 0.00 2.57
66 67 3.623703 CACAACATGAATGGAGGGATGA 58.376 45.455 0.00 0.00 0.00 2.92
67 68 2.691526 CCACAACATGAATGGAGGGATG 59.308 50.000 0.00 0.00 35.33 3.51
68 69 2.312741 ACCACAACATGAATGGAGGGAT 59.687 45.455 17.66 0.00 36.94 3.85
69 70 1.710244 ACCACAACATGAATGGAGGGA 59.290 47.619 17.66 0.00 36.94 4.20
70 71 1.820519 CACCACAACATGAATGGAGGG 59.179 52.381 17.66 12.53 36.94 4.30
71 72 1.203052 GCACCACAACATGAATGGAGG 59.797 52.381 17.66 14.61 36.94 4.30
72 73 2.165167 AGCACCACAACATGAATGGAG 58.835 47.619 17.66 12.41 36.94 3.86
73 74 2.291209 AGCACCACAACATGAATGGA 57.709 45.000 17.66 0.00 36.94 3.41
74 75 6.210796 CAATATAGCACCACAACATGAATGG 58.789 40.000 0.00 6.40 39.57 3.16
75 76 5.688621 GCAATATAGCACCACAACATGAATG 59.311 40.000 0.00 0.09 0.00 2.67
76 77 5.595542 AGCAATATAGCACCACAACATGAAT 59.404 36.000 0.00 0.00 36.85 2.57
77 78 4.949238 AGCAATATAGCACCACAACATGAA 59.051 37.500 0.00 0.00 36.85 2.57
78 79 4.525996 AGCAATATAGCACCACAACATGA 58.474 39.130 0.00 0.00 36.85 3.07
79 80 4.906065 AGCAATATAGCACCACAACATG 57.094 40.909 0.00 0.00 36.85 3.21
80 81 4.516698 GCTAGCAATATAGCACCACAACAT 59.483 41.667 10.63 0.00 46.12 2.71
81 82 3.876914 GCTAGCAATATAGCACCACAACA 59.123 43.478 10.63 0.00 46.12 3.33
82 83 4.474226 GCTAGCAATATAGCACCACAAC 57.526 45.455 10.63 0.00 46.12 3.32
90 91 1.710339 GGCGCGCTAGCAATATAGC 59.290 57.895 32.29 7.75 45.49 2.97
91 92 0.456142 TCGGCGCGCTAGCAATATAG 60.456 55.000 32.29 9.31 45.49 1.31
92 93 0.038983 TTCGGCGCGCTAGCAATATA 60.039 50.000 32.29 5.47 45.49 0.86
93 94 1.284982 CTTCGGCGCGCTAGCAATAT 61.285 55.000 32.29 0.00 45.49 1.28
94 95 1.949133 CTTCGGCGCGCTAGCAATA 60.949 57.895 32.29 6.59 45.49 1.90
95 96 3.264897 CTTCGGCGCGCTAGCAAT 61.265 61.111 32.29 0.00 45.49 3.56
99 100 1.734477 ATATGCTTCGGCGCGCTAG 60.734 57.895 32.29 24.43 45.37 3.42
100 101 2.021584 CATATGCTTCGGCGCGCTA 61.022 57.895 32.29 17.14 45.37 4.26
101 102 3.341043 CATATGCTTCGGCGCGCT 61.341 61.111 32.29 11.94 45.37 5.92
102 103 3.640000 ACATATGCTTCGGCGCGC 61.640 61.111 25.94 25.94 45.37 6.86
103 104 2.035617 AACACATATGCTTCGGCGCG 62.036 55.000 0.00 0.00 45.37 6.86
104 105 0.098728 AAACACATATGCTTCGGCGC 59.901 50.000 0.00 0.00 45.37 6.53
105 106 3.878086 ATAAACACATATGCTTCGGCG 57.122 42.857 0.00 0.00 45.37 6.46
106 107 4.036262 TGGAATAAACACATATGCTTCGGC 59.964 41.667 1.58 0.00 42.19 5.54
107 108 5.749596 TGGAATAAACACATATGCTTCGG 57.250 39.130 1.58 0.00 0.00 4.30
108 109 7.194607 AGATGGAATAAACACATATGCTTCG 57.805 36.000 1.58 0.00 0.00 3.79
109 110 9.884465 GTAAGATGGAATAAACACATATGCTTC 57.116 33.333 1.58 0.00 0.00 3.86
110 111 9.632638 AGTAAGATGGAATAAACACATATGCTT 57.367 29.630 1.58 0.00 0.00 3.91
111 112 9.632638 AAGTAAGATGGAATAAACACATATGCT 57.367 29.630 1.58 0.00 0.00 3.79
112 113 9.669353 CAAGTAAGATGGAATAAACACATATGC 57.331 33.333 1.58 0.00 0.00 3.14
117 118 9.513906 TCAATCAAGTAAGATGGAATAAACACA 57.486 29.630 0.00 0.00 0.00 3.72
148 149 8.897752 GGAATTTGTTCTGAAACAGCTATCTAT 58.102 33.333 0.00 0.00 45.72 1.98
149 150 7.882791 TGGAATTTGTTCTGAAACAGCTATCTA 59.117 33.333 0.00 0.00 45.72 1.98
150 151 6.716628 TGGAATTTGTTCTGAAACAGCTATCT 59.283 34.615 0.00 0.00 45.72 1.98
151 152 6.913170 TGGAATTTGTTCTGAAACAGCTATC 58.087 36.000 0.00 0.00 45.72 2.08
152 153 6.899393 TGGAATTTGTTCTGAAACAGCTAT 57.101 33.333 0.00 0.00 45.72 2.97
153 154 6.716628 AGATGGAATTTGTTCTGAAACAGCTA 59.283 34.615 0.00 0.00 45.72 3.32
154 155 5.537674 AGATGGAATTTGTTCTGAAACAGCT 59.462 36.000 0.00 0.00 45.72 4.24
155 156 5.776744 AGATGGAATTTGTTCTGAAACAGC 58.223 37.500 0.00 0.00 45.72 4.40
156 157 8.571336 AGTAAGATGGAATTTGTTCTGAAACAG 58.429 33.333 0.00 0.00 45.72 3.16
157 158 8.463930 AGTAAGATGGAATTTGTTCTGAAACA 57.536 30.769 0.00 0.00 43.58 2.83
158 159 9.185192 CAAGTAAGATGGAATTTGTTCTGAAAC 57.815 33.333 0.00 0.00 35.85 2.78
159 160 9.130661 TCAAGTAAGATGGAATTTGTTCTGAAA 57.869 29.630 0.00 0.00 0.00 2.69
160 161 8.690203 TCAAGTAAGATGGAATTTGTTCTGAA 57.310 30.769 0.00 0.00 0.00 3.02
161 162 8.868522 ATCAAGTAAGATGGAATTTGTTCTGA 57.131 30.769 0.00 0.00 0.00 3.27
162 163 9.350357 CAATCAAGTAAGATGGAATTTGTTCTG 57.650 33.333 0.00 0.00 0.00 3.02
163 164 9.300681 TCAATCAAGTAAGATGGAATTTGTTCT 57.699 29.630 0.00 0.00 0.00 3.01
164 165 9.912634 TTCAATCAAGTAAGATGGAATTTGTTC 57.087 29.630 0.00 0.00 33.96 3.18
282 283 7.379529 GGCATCCAATATGTATGAAAACTTTCG 59.620 37.037 0.00 0.00 40.01 3.46
288 289 6.040729 CCTGTGGCATCCAATATGTATGAAAA 59.959 38.462 0.00 0.00 34.18 2.29
292 293 3.760151 CCCTGTGGCATCCAATATGTATG 59.240 47.826 0.00 0.00 34.18 2.39
294 295 3.052329 TCCCTGTGGCATCCAATATGTA 58.948 45.455 0.00 0.00 34.18 2.29
296 297 2.662535 TCCCTGTGGCATCCAATATG 57.337 50.000 0.00 0.00 34.18 1.78
297 298 3.503365 CATTCCCTGTGGCATCCAATAT 58.497 45.455 0.00 0.00 34.18 1.28
298 299 2.424667 CCATTCCCTGTGGCATCCAATA 60.425 50.000 0.00 0.00 34.18 1.90
312 313 4.322725 GGGTTCAAATTTCAGTCCATTCCC 60.323 45.833 0.00 0.00 0.00 3.97
313 314 4.283212 TGGGTTCAAATTTCAGTCCATTCC 59.717 41.667 0.00 0.00 0.00 3.01
327 328 6.968263 TGACACTTATCATTTGGGTTCAAA 57.032 33.333 0.00 0.00 45.61 2.69
355 356 1.080772 CGGAGTGCTTCGTGCTACA 60.081 57.895 5.00 0.00 43.37 2.74
356 357 1.080705 ACGGAGTGCTTCGTGCTAC 60.081 57.895 4.56 2.58 42.51 3.58
357 358 3.362262 ACGGAGTGCTTCGTGCTA 58.638 55.556 4.56 0.00 42.51 3.49
391 392 7.781056 TCTCTTTTCAAATGGCAACTTTAGTT 58.219 30.769 0.00 0.00 39.12 2.24
402 403 6.038161 GGGGTTTGTTTTCTCTTTTCAAATGG 59.962 38.462 0.00 0.00 32.16 3.16
406 407 5.092554 GGGGGTTTGTTTTCTCTTTTCAA 57.907 39.130 0.00 0.00 0.00 2.69
407 408 4.746535 GGGGGTTTGTTTTCTCTTTTCA 57.253 40.909 0.00 0.00 0.00 2.69
425 426 2.741553 GCAAGTTTCAGTGTTTTGGGGG 60.742 50.000 0.00 0.00 0.00 5.40
426 427 2.549926 GCAAGTTTCAGTGTTTTGGGG 58.450 47.619 0.00 0.00 0.00 4.96
434 435 5.350914 TGTTTTTGAATGGCAAGTTTCAGTG 59.649 36.000 0.00 0.00 37.87 3.66
435 436 5.486526 TGTTTTTGAATGGCAAGTTTCAGT 58.513 33.333 0.00 0.00 37.87 3.41
484 486 6.174720 AGTTTAGTGAAGTGAGGATGACAA 57.825 37.500 0.00 0.00 0.00 3.18
487 489 6.174720 ACAAGTTTAGTGAAGTGAGGATGA 57.825 37.500 0.00 0.00 0.00 2.92
508 510 7.776107 TGACAACTCCAAACATTTTTATGACA 58.224 30.769 0.00 0.00 0.00 3.58
519 521 7.223971 GCTACGAATATATGACAACTCCAAACA 59.776 37.037 0.00 0.00 0.00 2.83
524 526 6.144080 GTGTGCTACGAATATATGACAACTCC 59.856 42.308 0.00 0.00 0.00 3.85
525 527 7.095024 GTGTGCTACGAATATATGACAACTC 57.905 40.000 0.00 0.00 0.00 3.01
541 543 1.578583 AAGAACCACACGTGTGCTAC 58.421 50.000 37.33 27.99 44.34 3.58
542 544 3.006003 TGATAAGAACCACACGTGTGCTA 59.994 43.478 37.33 23.02 44.34 3.49
543 545 2.224185 TGATAAGAACCACACGTGTGCT 60.224 45.455 37.33 27.28 44.34 4.40
544 546 2.139917 TGATAAGAACCACACGTGTGC 58.860 47.619 37.33 25.66 44.34 4.57
545 547 3.807622 ACTTGATAAGAACCACACGTGTG 59.192 43.478 36.13 36.13 45.23 3.82
546 548 4.067972 ACTTGATAAGAACCACACGTGT 57.932 40.909 17.22 17.22 0.00 4.49
547 549 6.367695 TGATTACTTGATAAGAACCACACGTG 59.632 38.462 15.48 15.48 0.00 4.49
548 550 6.460781 TGATTACTTGATAAGAACCACACGT 58.539 36.000 0.00 0.00 0.00 4.49
549 551 6.036083 CCTGATTACTTGATAAGAACCACACG 59.964 42.308 0.00 0.00 0.00 4.49
556 558 6.884472 TGGACCCTGATTACTTGATAAGAA 57.116 37.500 0.00 0.00 0.00 2.52
557 559 6.443849 AGTTGGACCCTGATTACTTGATAAGA 59.556 38.462 0.00 0.00 0.00 2.10
558 560 6.653989 AGTTGGACCCTGATTACTTGATAAG 58.346 40.000 0.00 0.00 0.00 1.73
568 570 4.714308 TGTTTTTCAAGTTGGACCCTGATT 59.286 37.500 2.34 0.00 0.00 2.57
570 572 3.702792 TGTTTTTCAAGTTGGACCCTGA 58.297 40.909 2.34 0.00 0.00 3.86
581 583 4.675146 CGGCCCTCATACATGTTTTTCAAG 60.675 45.833 2.30 0.00 0.00 3.02
584 586 2.752903 ACGGCCCTCATACATGTTTTTC 59.247 45.455 2.30 0.00 0.00 2.29
585 587 2.491693 CACGGCCCTCATACATGTTTTT 59.508 45.455 2.30 0.00 0.00 1.94
691 701 5.619086 GCAGCATAGAAAATTACGGTGTTGT 60.619 40.000 0.00 0.00 0.00 3.32
727 737 6.013206 TCCATTTCTTACTTGGTTACTGGCTA 60.013 38.462 0.00 0.00 0.00 3.93
751 778 5.983540 AGAAACTGATGGACTAATGGTCTC 58.016 41.667 0.00 0.00 43.97 3.36
856 892 0.109964 TTCGCGGCAATTTGTAGTGC 60.110 50.000 6.13 0.00 44.29 4.40
905 954 4.453480 AACTTTGACCAGGAAGGAATGA 57.547 40.909 0.00 0.00 41.22 2.57
906 955 6.648879 TTAAACTTTGACCAGGAAGGAATG 57.351 37.500 0.00 0.00 41.22 2.67
907 956 7.010160 TGATTAAACTTTGACCAGGAAGGAAT 58.990 34.615 0.00 0.00 41.22 3.01
908 957 6.369629 TGATTAAACTTTGACCAGGAAGGAA 58.630 36.000 0.00 0.00 41.22 3.36
918 967 6.151691 TGCTGCAAGATGATTAAACTTTGAC 58.848 36.000 0.00 0.00 34.07 3.18
983 1150 1.331138 GCATGATGAGCTGAGTTGAGC 59.669 52.381 0.00 0.00 39.46 4.26
1061 1233 2.425773 CGTCGTCGTTTCCGTCGT 60.426 61.111 0.00 0.00 44.09 4.34
1380 1552 1.025113 CGCTGTCGTCTACCTCCAGA 61.025 60.000 0.00 0.00 0.00 3.86
1388 1560 4.156622 CGCCGTCGCTGTCGTCTA 62.157 66.667 0.00 0.00 36.96 2.59
1427 1599 2.509336 GGCAGACCGGACACATCG 60.509 66.667 9.46 0.00 0.00 3.84
1452 1624 1.885388 CATTTCGCCGCCGTGGATA 60.885 57.895 0.88 0.00 42.00 2.59
1663 1838 4.503741 ACGTGCATGTTTTAGAGCAAAT 57.496 36.364 5.51 0.00 38.91 2.32
1745 1920 0.591659 GCAGAAAAACCGACTGACCC 59.408 55.000 0.00 0.00 34.07 4.46
1747 1922 1.264288 CTGGCAGAAAAACCGACTGAC 59.736 52.381 9.42 0.00 39.78 3.51
1748 1923 1.134220 ACTGGCAGAAAAACCGACTGA 60.134 47.619 23.66 0.00 34.07 3.41
1749 1924 1.308998 ACTGGCAGAAAAACCGACTG 58.691 50.000 23.66 0.00 35.14 3.51
1750 1925 1.676006 CAACTGGCAGAAAAACCGACT 59.324 47.619 23.66 0.00 0.00 4.18
1751 1926 1.673920 TCAACTGGCAGAAAAACCGAC 59.326 47.619 23.66 0.00 0.00 4.79
1752 1927 2.045561 TCAACTGGCAGAAAAACCGA 57.954 45.000 23.66 3.51 0.00 4.69
1754 1929 2.802247 GCAATCAACTGGCAGAAAAACC 59.198 45.455 23.66 0.00 0.00 3.27
1827 2006 5.774690 ACAGGTCACCATACAACATGAAAAT 59.225 36.000 0.00 0.00 0.00 1.82
1892 3838 9.613428 CATCCAATGTAGAGATACACCTAAAAA 57.387 33.333 0.00 0.00 32.16 1.94
1894 3840 8.547481 TCATCCAATGTAGAGATACACCTAAA 57.453 34.615 0.00 0.00 32.16 1.85
1895 3841 8.547481 TTCATCCAATGTAGAGATACACCTAA 57.453 34.615 0.00 0.00 32.16 2.69
1896 3842 8.727100 ATTCATCCAATGTAGAGATACACCTA 57.273 34.615 0.00 0.00 32.16 3.08
1897 3843 7.512058 AGATTCATCCAATGTAGAGATACACCT 59.488 37.037 0.00 0.00 32.16 4.00
1898 3844 7.601886 CAGATTCATCCAATGTAGAGATACACC 59.398 40.741 0.00 0.00 32.16 4.16
1899 3845 7.117523 GCAGATTCATCCAATGTAGAGATACAC 59.882 40.741 0.00 0.00 32.16 2.90
1900 3846 7.015974 AGCAGATTCATCCAATGTAGAGATACA 59.984 37.037 0.00 0.00 0.00 2.29
1901 3847 7.385267 AGCAGATTCATCCAATGTAGAGATAC 58.615 38.462 0.00 0.00 0.00 2.24
1904 3850 5.883685 AGCAGATTCATCCAATGTAGAGA 57.116 39.130 0.00 0.00 0.00 3.10
1905 3851 7.613585 AGATAGCAGATTCATCCAATGTAGAG 58.386 38.462 0.00 0.00 0.00 2.43
1906 3852 7.454066 AGAGATAGCAGATTCATCCAATGTAGA 59.546 37.037 0.00 0.00 0.00 2.59
1907 3853 7.613585 AGAGATAGCAGATTCATCCAATGTAG 58.386 38.462 0.00 0.00 0.00 2.74
1908 3854 7.550597 AGAGATAGCAGATTCATCCAATGTA 57.449 36.000 0.00 0.00 0.00 2.29
1909 3855 6.436738 AGAGATAGCAGATTCATCCAATGT 57.563 37.500 0.00 0.00 0.00 2.71
1910 3856 7.384477 TGTAGAGATAGCAGATTCATCCAATG 58.616 38.462 0.00 0.00 0.00 2.82
1911 3857 7.550597 TGTAGAGATAGCAGATTCATCCAAT 57.449 36.000 0.00 0.00 0.00 3.16
1912 3858 6.983906 TGTAGAGATAGCAGATTCATCCAA 57.016 37.500 0.00 0.00 0.00 3.53
1913 3859 7.384477 CAATGTAGAGATAGCAGATTCATCCA 58.616 38.462 0.00 0.00 0.00 3.41
1914 3860 6.817641 CCAATGTAGAGATAGCAGATTCATCC 59.182 42.308 0.00 0.00 0.00 3.51
1915 3861 6.313411 GCCAATGTAGAGATAGCAGATTCATC 59.687 42.308 0.00 0.00 0.00 2.92
1916 3862 6.013553 AGCCAATGTAGAGATAGCAGATTCAT 60.014 38.462 0.00 0.00 0.00 2.57
1917 3863 5.306419 AGCCAATGTAGAGATAGCAGATTCA 59.694 40.000 0.00 0.00 0.00 2.57
1918 3864 5.638657 CAGCCAATGTAGAGATAGCAGATTC 59.361 44.000 0.00 0.00 0.00 2.52
1919 3865 5.306419 TCAGCCAATGTAGAGATAGCAGATT 59.694 40.000 0.00 0.00 0.00 2.40
1920 3866 4.837298 TCAGCCAATGTAGAGATAGCAGAT 59.163 41.667 0.00 0.00 0.00 2.90
1921 3867 4.218312 TCAGCCAATGTAGAGATAGCAGA 58.782 43.478 0.00 0.00 0.00 4.26
1922 3868 4.558178 CTCAGCCAATGTAGAGATAGCAG 58.442 47.826 0.00 0.00 0.00 4.24
1923 3869 3.323115 CCTCAGCCAATGTAGAGATAGCA 59.677 47.826 0.00 0.00 0.00 3.49
1924 3870 3.864160 GCCTCAGCCAATGTAGAGATAGC 60.864 52.174 0.00 0.00 0.00 2.97
1925 3871 3.924144 GCCTCAGCCAATGTAGAGATAG 58.076 50.000 0.00 0.00 0.00 2.08
1927 3873 2.926778 GCCTCAGCCAATGTAGAGAT 57.073 50.000 0.00 0.00 0.00 2.75
1954 3900 2.048603 GGCTAGCTTGGTTGCCCAG 61.049 63.158 15.72 0.00 43.15 4.45
1967 3913 4.285020 TCAGATGGGCTAGATATGGCTAG 58.715 47.826 0.00 0.00 40.62 3.42
1973 3919 4.665009 TGGGTTTTCAGATGGGCTAGATAT 59.335 41.667 0.00 0.00 0.00 1.63
2059 4005 2.470821 GTGATATGTGACGGTGGCTAC 58.529 52.381 0.00 0.00 0.00 3.58
2069 4015 1.754226 TGCCTAGCACGTGATATGTGA 59.246 47.619 22.23 2.89 37.29 3.58
2086 4032 1.283321 AGGAAATTCTGGGAGAGTGCC 59.717 52.381 0.00 0.00 0.00 5.01
2089 4035 9.997172 AATAAATAAAGGAAATTCTGGGAGAGT 57.003 29.630 0.00 0.00 0.00 3.24
2235 4187 1.002900 CGTGCCTCAGCGAAAGAAAAA 60.003 47.619 0.00 0.00 44.31 1.94
2236 4188 0.586319 CGTGCCTCAGCGAAAGAAAA 59.414 50.000 0.00 0.00 44.31 2.29
2237 4189 1.227999 CCGTGCCTCAGCGAAAGAAA 61.228 55.000 0.00 0.00 44.31 2.52
2238 4190 1.667830 CCGTGCCTCAGCGAAAGAA 60.668 57.895 0.00 0.00 44.31 2.52
2239 4191 1.888436 ATCCGTGCCTCAGCGAAAGA 61.888 55.000 0.00 0.00 44.31 2.52
2240 4192 1.021390 AATCCGTGCCTCAGCGAAAG 61.021 55.000 0.00 0.00 44.31 2.62
2254 4206 2.810650 CCTCCACGAGAACTAAATCCG 58.189 52.381 0.00 0.00 0.00 4.18
2344 4299 1.407656 ATCTATGGCTCCCGCGGAAA 61.408 55.000 30.73 13.89 36.88 3.13
2351 4306 4.809070 GGCACATCTATGGCTCCC 57.191 61.111 0.00 0.00 41.78 4.30
2408 4363 3.609373 CACGAAAGCAAATATGTGCCTTG 59.391 43.478 14.50 8.50 46.14 3.61
2409 4364 3.505680 TCACGAAAGCAAATATGTGCCTT 59.494 39.130 14.50 7.90 46.14 4.35
2433 4388 4.385358 TTTTCTTTTCCAAGAGGCACAC 57.615 40.909 0.00 0.00 40.28 3.82
2471 4426 9.778741 TTCACAAGAAGTAAATATGTGTCTCTT 57.221 29.630 4.37 0.00 41.52 2.85
2504 4459 6.385649 TTTTACTTTTTCGAGAGGCACAAT 57.614 33.333 0.00 0.00 0.00 2.71
2517 4472 8.535690 TTGGAAAACGTGTCATTTTACTTTTT 57.464 26.923 0.00 0.00 32.06 1.94
2556 4511 4.690748 CGAGAAGTAAATTTGTGCCTCTCA 59.309 41.667 0.00 0.00 0.00 3.27
2559 4514 4.378459 CCACGAGAAGTAAATTTGTGCCTC 60.378 45.833 0.00 2.27 0.00 4.70
2560 4515 3.502211 CCACGAGAAGTAAATTTGTGCCT 59.498 43.478 0.00 0.00 0.00 4.75
2563 4518 4.698276 CGTCCACGAGAAGTAAATTTGTG 58.302 43.478 0.00 0.00 43.02 3.33
2564 4519 3.185797 GCGTCCACGAGAAGTAAATTTGT 59.814 43.478 2.58 0.00 43.02 2.83
2565 4520 3.185594 TGCGTCCACGAGAAGTAAATTTG 59.814 43.478 2.58 0.00 43.02 2.32
2566 4521 3.185797 GTGCGTCCACGAGAAGTAAATTT 59.814 43.478 2.58 0.00 43.02 1.82
2586 4541 0.877071 AGCGTGGAAGCAAATCTGTG 59.123 50.000 0.00 0.00 40.15 3.66
2623 4578 8.894768 TCAAGGAAAAAGAAAAAGAAAACACA 57.105 26.923 0.00 0.00 0.00 3.72
2624 4579 9.203421 TCTCAAGGAAAAAGAAAAAGAAAACAC 57.797 29.630 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.