Multiple sequence alignment - TraesCS5B01G375700

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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 TraesCS5B01G375700 chr5B 100.000 2877 0 0 1 2877 553186770 553183894 0.000000e+00 5313
1 TraesCS5B01G375700 chr5B 94.234 607 27 5 2279 2877 89742934 89743540 0.000000e+00 920
2 TraesCS5B01G375700 chr5B 80.591 237 43 3 435 669 678022479 678022244 2.280000e-41 180
3 TraesCS5B01G375700 chr5B 81.188 202 32 5 423 621 608213710 608213908 1.070000e-34 158
4 TraesCS5B01G375700 chr5D 90.967 1406 52 28 876 2254 452681948 452680591 0.000000e+00 1823
5 TraesCS5B01G375700 chr5D 86.811 599 54 16 251 839 452682606 452682023 0.000000e+00 645
6 TraesCS5B01G375700 chr5D 81.132 265 33 13 1 259 559097890 559097637 2.260000e-46 196
7 TraesCS5B01G375700 chr5D 76.172 256 24 18 1 254 80187010 80187230 1.820000e-17 100
8 TraesCS5B01G375700 chr5A 92.041 1181 52 21 920 2075 571685586 571684423 0.000000e+00 1622
9 TraesCS5B01G375700 chr5A 92.632 190 13 1 2066 2254 571684376 571684187 3.650000e-69 272
10 TraesCS5B01G375700 chr5A 83.133 166 22 6 92 254 615921680 615921842 2.310000e-31 147
11 TraesCS5B01G375700 chr7B 95.537 605 20 5 2280 2877 66170680 66170076 0.000000e+00 961
12 TraesCS5B01G375700 chr7B 94.901 608 23 5 2278 2877 439997019 439997626 0.000000e+00 944
13 TraesCS5B01G375700 chr7B 94.711 605 24 5 2281 2877 192454531 192453927 0.000000e+00 933
14 TraesCS5B01G375700 chr7B 94.137 614 27 6 2272 2877 747024462 747023850 0.000000e+00 926
15 TraesCS5B01G375700 chr2B 95.199 604 19 6 2283 2877 229782057 229782659 0.000000e+00 946
16 TraesCS5B01G375700 chr4B 94.745 609 24 5 2277 2877 133610957 133611565 0.000000e+00 941
17 TraesCS5B01G375700 chr4B 79.394 165 24 4 511 668 404853633 404853472 1.090000e-19 108
18 TraesCS5B01G375700 chr4A 94.711 605 24 5 2281 2877 701948076 701947472 0.000000e+00 933
19 TraesCS5B01G375700 chr4A 81.526 249 36 8 428 668 514421572 514421818 2.260000e-46 196
20 TraesCS5B01G375700 chr4A 83.636 165 19 5 94 256 541880051 541879893 6.420000e-32 148
21 TraesCS5B01G375700 chr4A 79.592 147 24 4 526 671 631975267 631975408 1.820000e-17 100
22 TraesCS5B01G375700 chr3B 94.693 603 24 5 2283 2877 779374998 779374396 0.000000e+00 929
23 TraesCS5B01G375700 chr3B 85.441 261 31 5 1 258 157635774 157635518 6.110000e-67 265
24 TraesCS5B01G375700 chr6B 82.422 256 40 4 3 254 683575292 683575546 4.830000e-53 219
25 TraesCS5B01G375700 chr6B 85.222 203 23 7 58 254 472714234 472714435 4.860000e-48 202
26 TraesCS5B01G375700 chr1B 94.118 136 8 0 2120 2255 440500426 440500561 1.040000e-49 207
27 TraesCS5B01G375700 chr6D 82.083 240 35 7 435 669 38895048 38894812 6.290000e-47 198
28 TraesCS5B01G375700 chr7D 81.667 240 30 8 431 669 312574071 312573845 1.360000e-43 187
29 TraesCS5B01G375700 chr7D 83.636 165 21 5 94 255 21962606 21962445 1.790000e-32 150
30 TraesCS5B01G375700 chr7D 81.081 185 31 3 430 613 495853785 495853604 8.310000e-31 145
31 TraesCS5B01G375700 chr7D 82.432 148 20 5 523 668 58864637 58864494 1.080000e-24 124
32 TraesCS5B01G375700 chr3A 81.013 237 41 4 435 669 690899265 690899499 4.900000e-43 185
33 TraesCS5B01G375700 chr4D 87.755 147 13 4 112 254 465974457 465974602 1.770000e-37 167
34 TraesCS5B01G375700 chr4D 88.235 85 10 0 585 669 40400331 40400415 5.070000e-18 102
35 TraesCS5B01G375700 chr7A 80.263 228 31 7 427 653 225061610 225061396 2.970000e-35 159
36 TraesCS5B01G375700 chr2D 81.500 200 26 10 66 257 168430486 168430682 1.380000e-33 154
37 TraesCS5B01G375700 chr2D 84.375 160 21 3 100 256 481950230 481950072 1.380000e-33 154
38 TraesCS5B01G375700 chr1D 77.824 239 34 10 435 669 430064996 430064773 2.330000e-26 130


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 TraesCS5B01G375700 chr5B 553183894 553186770 2876 True 5313 5313 100.0000 1 2877 1 chr5B.!!$R1 2876
1 TraesCS5B01G375700 chr5B 89742934 89743540 606 False 920 920 94.2340 2279 2877 1 chr5B.!!$F1 598
2 TraesCS5B01G375700 chr5D 452680591 452682606 2015 True 1234 1823 88.8890 251 2254 2 chr5D.!!$R2 2003
3 TraesCS5B01G375700 chr5A 571684187 571685586 1399 True 947 1622 92.3365 920 2254 2 chr5A.!!$R1 1334
4 TraesCS5B01G375700 chr7B 66170076 66170680 604 True 961 961 95.5370 2280 2877 1 chr7B.!!$R1 597
5 TraesCS5B01G375700 chr7B 439997019 439997626 607 False 944 944 94.9010 2278 2877 1 chr7B.!!$F1 599
6 TraesCS5B01G375700 chr7B 192453927 192454531 604 True 933 933 94.7110 2281 2877 1 chr7B.!!$R2 596
7 TraesCS5B01G375700 chr7B 747023850 747024462 612 True 926 926 94.1370 2272 2877 1 chr7B.!!$R3 605
8 TraesCS5B01G375700 chr2B 229782057 229782659 602 False 946 946 95.1990 2283 2877 1 chr2B.!!$F1 594
9 TraesCS5B01G375700 chr4B 133610957 133611565 608 False 941 941 94.7450 2277 2877 1 chr4B.!!$F1 600
10 TraesCS5B01G375700 chr4A 701947472 701948076 604 True 933 933 94.7110 2281 2877 1 chr4A.!!$R2 596
11 TraesCS5B01G375700 chr3B 779374396 779374998 602 True 929 929 94.6930 2283 2877 1 chr3B.!!$R2 594

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
75 76 0.0293 CGATAGTGGGCCAATTTGCG 59.971 55.0 13.49 10.09 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2019 0.306228 TTGTTTGACACGCATGACCG 59.694 50.0 0.0 0.0 0.0 4.79 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
18 19 3.470520 CTGTTGAATTTGCGCCGAA 57.529 47.368 4.18 0.00 0.00 4.30
19 20 1.330306 CTGTTGAATTTGCGCCGAAG 58.670 50.000 4.18 0.00 0.00 3.79
20 21 0.662970 TGTTGAATTTGCGCCGAAGC 60.663 50.000 4.18 0.00 37.71 3.86
21 22 0.662970 GTTGAATTTGCGCCGAAGCA 60.663 50.000 4.18 0.67 46.54 3.91
30 31 2.126071 GCCGAAGCACGCAGACTA 60.126 61.111 0.00 0.00 41.07 2.59
31 32 1.519455 GCCGAAGCACGCAGACTAT 60.519 57.895 0.00 0.00 41.07 2.12
32 33 1.756375 GCCGAAGCACGCAGACTATG 61.756 60.000 0.00 0.00 41.07 2.23
33 34 1.148157 CCGAAGCACGCAGACTATGG 61.148 60.000 0.00 0.00 41.07 2.74
34 35 1.148157 CGAAGCACGCAGACTATGGG 61.148 60.000 0.00 0.00 46.92 4.00
35 36 1.432270 GAAGCACGCAGACTATGGGC 61.432 60.000 0.00 0.00 45.49 5.36
36 37 2.876368 AAGCACGCAGACTATGGGCC 62.876 60.000 0.00 0.00 45.49 5.80
37 38 2.586079 CACGCAGACTATGGGCCG 60.586 66.667 0.00 0.00 45.49 6.13
38 39 2.758327 ACGCAGACTATGGGCCGA 60.758 61.111 0.00 0.00 45.49 5.54
39 40 2.355986 ACGCAGACTATGGGCCGAA 61.356 57.895 0.00 0.00 45.49 4.30
40 41 1.153449 CGCAGACTATGGGCCGAAA 60.153 57.895 0.00 0.00 34.77 3.46
41 42 0.532862 CGCAGACTATGGGCCGAAAT 60.533 55.000 0.00 0.00 34.77 2.17
42 43 1.680338 GCAGACTATGGGCCGAAATT 58.320 50.000 0.00 0.00 0.00 1.82
43 44 1.334869 GCAGACTATGGGCCGAAATTG 59.665 52.381 0.00 0.00 0.00 2.32
44 45 1.949525 CAGACTATGGGCCGAAATTGG 59.050 52.381 0.00 0.00 0.00 3.16
45 46 1.564348 AGACTATGGGCCGAAATTGGT 59.436 47.619 0.00 0.00 0.00 3.67
46 47 1.947456 GACTATGGGCCGAAATTGGTC 59.053 52.381 0.00 0.00 0.00 4.02
47 48 1.283613 ACTATGGGCCGAAATTGGTCA 59.716 47.619 0.00 0.00 34.42 4.02
48 49 2.291282 ACTATGGGCCGAAATTGGTCAA 60.291 45.455 0.00 0.00 34.42 3.18
49 50 1.864669 ATGGGCCGAAATTGGTCAAT 58.135 45.000 0.00 0.00 34.42 2.57
50 51 1.638529 TGGGCCGAAATTGGTCAATT 58.361 45.000 0.00 3.34 42.35 2.32
62 63 6.455360 AATTGGTCAATTTGCATCGATAGT 57.545 33.333 0.00 0.00 37.74 2.12
63 64 4.880886 TGGTCAATTTGCATCGATAGTG 57.119 40.909 0.00 0.00 37.40 2.74
64 65 3.627123 TGGTCAATTTGCATCGATAGTGG 59.373 43.478 0.00 0.00 37.40 4.00
65 66 3.003689 GGTCAATTTGCATCGATAGTGGG 59.996 47.826 0.00 0.00 37.40 4.61
66 67 2.618241 TCAATTTGCATCGATAGTGGGC 59.382 45.455 0.00 0.00 37.40 5.36
67 68 1.609208 ATTTGCATCGATAGTGGGCC 58.391 50.000 0.00 0.00 37.40 5.80
68 69 0.254462 TTTGCATCGATAGTGGGCCA 59.746 50.000 0.00 0.00 37.40 5.36
69 70 0.254462 TTGCATCGATAGTGGGCCAA 59.746 50.000 8.40 0.00 37.40 4.52
70 71 0.473755 TGCATCGATAGTGGGCCAAT 59.526 50.000 12.68 12.68 37.40 3.16
71 72 1.133823 TGCATCGATAGTGGGCCAATT 60.134 47.619 13.49 4.12 37.40 2.32
72 73 1.956477 GCATCGATAGTGGGCCAATTT 59.044 47.619 13.49 3.52 37.40 1.82
73 74 2.287788 GCATCGATAGTGGGCCAATTTG 60.288 50.000 13.49 2.31 37.40 2.32
74 75 1.388547 TCGATAGTGGGCCAATTTGC 58.611 50.000 13.49 0.00 37.40 3.68
75 76 0.029300 CGATAGTGGGCCAATTTGCG 59.971 55.000 13.49 10.09 0.00 4.85
76 77 0.249031 GATAGTGGGCCAATTTGCGC 60.249 55.000 13.49 11.18 43.84 6.09
77 78 1.675720 ATAGTGGGCCAATTTGCGCC 61.676 55.000 13.49 16.24 42.99 6.53
80 81 3.837112 GGGCCAATTTGCGCCGAT 61.837 61.111 4.39 0.00 46.73 4.18
81 82 2.485795 GGGCCAATTTGCGCCGATA 61.486 57.895 4.39 0.00 46.73 2.92
82 83 1.435515 GGCCAATTTGCGCCGATAA 59.564 52.632 4.18 0.00 34.94 1.75
83 84 0.031994 GGCCAATTTGCGCCGATAAT 59.968 50.000 4.18 0.00 34.94 1.28
84 85 1.268352 GGCCAATTTGCGCCGATAATA 59.732 47.619 4.18 0.00 34.94 0.98
85 86 2.584791 GCCAATTTGCGCCGATAATAG 58.415 47.619 4.18 0.00 0.00 1.73
86 87 2.225491 GCCAATTTGCGCCGATAATAGA 59.775 45.455 4.18 0.00 0.00 1.98
87 88 3.810373 CCAATTTGCGCCGATAATAGAC 58.190 45.455 4.18 0.00 0.00 2.59
88 89 3.498397 CCAATTTGCGCCGATAATAGACT 59.502 43.478 4.18 0.00 0.00 3.24
89 90 4.457810 CAATTTGCGCCGATAATAGACTG 58.542 43.478 4.18 0.00 0.00 3.51
90 91 3.446310 TTTGCGCCGATAATAGACTGA 57.554 42.857 4.18 0.00 0.00 3.41
91 92 3.446310 TTGCGCCGATAATAGACTGAA 57.554 42.857 4.18 0.00 0.00 3.02
92 93 3.446310 TGCGCCGATAATAGACTGAAA 57.554 42.857 4.18 0.00 0.00 2.69
93 94 3.787785 TGCGCCGATAATAGACTGAAAA 58.212 40.909 4.18 0.00 0.00 2.29
94 95 3.802139 TGCGCCGATAATAGACTGAAAAG 59.198 43.478 4.18 0.00 0.00 2.27
95 96 3.802685 GCGCCGATAATAGACTGAAAAGT 59.197 43.478 0.00 0.00 0.00 2.66
96 97 4.318121 GCGCCGATAATAGACTGAAAAGTG 60.318 45.833 0.00 0.00 0.00 3.16
97 98 4.209288 CGCCGATAATAGACTGAAAAGTGG 59.791 45.833 0.00 0.00 0.00 4.00
98 99 5.357257 GCCGATAATAGACTGAAAAGTGGA 58.643 41.667 0.00 0.00 0.00 4.02
99 100 5.234543 GCCGATAATAGACTGAAAAGTGGAC 59.765 44.000 0.00 0.00 0.00 4.02
100 101 5.753921 CCGATAATAGACTGAAAAGTGGACC 59.246 44.000 0.00 0.00 0.00 4.46
101 102 6.338146 CGATAATAGACTGAAAAGTGGACCA 58.662 40.000 0.00 0.00 0.00 4.02
102 103 6.816640 CGATAATAGACTGAAAAGTGGACCAA 59.183 38.462 0.00 0.00 0.00 3.67
103 104 7.495934 CGATAATAGACTGAAAAGTGGACCAAT 59.504 37.037 0.00 0.00 0.00 3.16
104 105 9.178758 GATAATAGACTGAAAAGTGGACCAATT 57.821 33.333 0.16 0.16 0.00 2.32
105 106 7.839680 AATAGACTGAAAAGTGGACCAATTT 57.160 32.000 14.02 14.02 33.01 1.82
106 107 5.520376 AGACTGAAAAGTGGACCAATTTG 57.480 39.130 19.90 10.58 32.02 2.32
107 108 4.051237 GACTGAAAAGTGGACCAATTTGC 58.949 43.478 19.90 18.41 32.02 3.68
108 109 3.052036 CTGAAAAGTGGACCAATTTGCG 58.948 45.455 19.90 10.86 30.53 4.85
109 110 1.792367 GAAAAGTGGACCAATTTGCGC 59.208 47.619 19.90 9.49 32.02 6.09
110 111 0.033366 AAAGTGGACCAATTTGCGCC 59.967 50.000 18.64 0.00 30.46 6.53
111 112 2.126502 GTGGACCAATTTGCGCCG 60.127 61.111 4.18 0.00 0.00 6.46
112 113 2.281831 TGGACCAATTTGCGCCGA 60.282 55.556 4.18 0.00 0.00 5.54
113 114 1.899054 TGGACCAATTTGCGCCGAA 60.899 52.632 4.18 0.00 0.00 4.30
114 115 1.287503 GGACCAATTTGCGCCGAAA 59.712 52.632 4.18 0.00 0.00 3.46
115 116 0.732538 GGACCAATTTGCGCCGAAAG 60.733 55.000 4.18 0.00 0.00 2.62
116 117 0.039527 GACCAATTTGCGCCGAAAGT 60.040 50.000 4.18 0.00 0.00 2.66
117 118 0.318614 ACCAATTTGCGCCGAAAGTG 60.319 50.000 4.18 9.37 32.09 3.16
118 119 1.008361 CCAATTTGCGCCGAAAGTGG 61.008 55.000 20.57 20.57 42.73 4.00
119 120 1.008361 CAATTTGCGCCGAAAGTGGG 61.008 55.000 4.18 0.00 29.36 4.61
125 126 2.981350 GCCGAAAGTGGGCCGAAA 60.981 61.111 0.00 0.00 44.97 3.46
126 127 2.340328 GCCGAAAGTGGGCCGAAAT 61.340 57.895 0.00 0.00 44.97 2.17
127 128 1.800681 CCGAAAGTGGGCCGAAATC 59.199 57.895 0.00 0.00 0.00 2.17
128 129 1.423845 CGAAAGTGGGCCGAAATCG 59.576 57.895 0.00 2.93 39.44 3.34
177 178 4.851179 GGAACCCGATCGCCCCAC 62.851 72.222 10.32 0.00 0.00 4.61
184 185 4.910585 GATCGCCCCACGCCGATT 62.911 66.667 0.00 0.00 43.48 3.34
185 186 4.483243 ATCGCCCCACGCCGATTT 62.483 61.111 0.00 0.00 40.95 2.17
186 187 3.987954 ATCGCCCCACGCCGATTTT 62.988 57.895 0.00 0.00 40.95 1.82
187 188 3.743636 CGCCCCACGCCGATTTTT 61.744 61.111 0.00 0.00 33.16 1.94
188 189 2.180769 GCCCCACGCCGATTTTTC 59.819 61.111 0.00 0.00 0.00 2.29
189 190 2.631580 GCCCCACGCCGATTTTTCA 61.632 57.895 0.00 0.00 0.00 2.69
190 191 1.506262 CCCCACGCCGATTTTTCAG 59.494 57.895 0.00 0.00 0.00 3.02
191 192 1.154035 CCCACGCCGATTTTTCAGC 60.154 57.895 0.00 0.00 0.00 4.26
192 193 1.154035 CCACGCCGATTTTTCAGCC 60.154 57.895 0.00 0.00 0.00 4.85
193 194 1.578926 CACGCCGATTTTTCAGCCA 59.421 52.632 0.00 0.00 0.00 4.75
194 195 0.039617 CACGCCGATTTTTCAGCCAA 60.040 50.000 0.00 0.00 0.00 4.52
195 196 0.039527 ACGCCGATTTTTCAGCCAAC 60.040 50.000 0.00 0.00 0.00 3.77
196 197 0.039617 CGCCGATTTTTCAGCCAACA 60.040 50.000 0.00 0.00 0.00 3.33
197 198 1.418373 GCCGATTTTTCAGCCAACAC 58.582 50.000 0.00 0.00 0.00 3.32
198 199 1.685302 CCGATTTTTCAGCCAACACG 58.315 50.000 0.00 0.00 0.00 4.49
199 200 1.052287 CGATTTTTCAGCCAACACGC 58.948 50.000 0.00 0.00 0.00 5.34
200 201 1.418373 GATTTTTCAGCCAACACGCC 58.582 50.000 0.00 0.00 0.00 5.68
201 202 0.033366 ATTTTTCAGCCAACACGCCC 59.967 50.000 0.00 0.00 0.00 6.13
202 203 2.022240 TTTTTCAGCCAACACGCCCC 62.022 55.000 0.00 0.00 0.00 5.80
203 204 4.966787 TTCAGCCAACACGCCCCC 62.967 66.667 0.00 0.00 0.00 5.40
216 217 4.954970 CCCCCATGCGGCGCTATT 62.955 66.667 33.26 14.96 0.00 1.73
217 218 2.906897 CCCCATGCGGCGCTATTT 60.907 61.111 33.26 12.27 0.00 1.40
218 219 2.489275 CCCCATGCGGCGCTATTTT 61.489 57.895 33.26 9.63 0.00 1.82
219 220 1.169661 CCCCATGCGGCGCTATTTTA 61.170 55.000 33.26 12.12 0.00 1.52
220 221 0.665835 CCCATGCGGCGCTATTTTAA 59.334 50.000 33.26 11.27 0.00 1.52
221 222 1.334960 CCCATGCGGCGCTATTTTAAG 60.335 52.381 33.26 8.21 0.00 1.85
222 223 1.398595 CATGCGGCGCTATTTTAAGC 58.601 50.000 33.26 0.00 39.21 3.09
230 231 0.668535 GCTATTTTAAGCGCCTGGGG 59.331 55.000 2.29 6.36 31.76 4.96
231 232 0.668535 CTATTTTAAGCGCCTGGGGC 59.331 55.000 26.54 26.54 46.75 5.80
247 248 3.190878 GCCAAACGGCTGGAGATG 58.809 61.111 9.09 0.00 46.85 2.90
248 249 3.056313 GCCAAACGGCTGGAGATGC 62.056 63.158 9.09 0.00 46.85 3.91
249 250 1.377725 CCAAACGGCTGGAGATGCT 60.378 57.895 0.00 0.00 38.96 3.79
255 256 1.134670 ACGGCTGGAGATGCTCTTAAC 60.135 52.381 0.00 0.00 0.00 2.01
262 263 5.724328 CTGGAGATGCTCTTAACTGTAACA 58.276 41.667 0.00 0.00 0.00 2.41
263 264 6.109156 TGGAGATGCTCTTAACTGTAACAA 57.891 37.500 0.00 0.00 0.00 2.83
279 280 1.452651 CAATGGCTGGAGTGGCGAT 60.453 57.895 0.00 0.00 35.06 4.58
285 286 1.271054 GGCTGGAGTGGCGATATCAAT 60.271 52.381 3.12 0.00 0.00 2.57
294 295 7.602644 TGGAGTGGCGATATCAATATTTAGTTC 59.397 37.037 3.12 0.00 0.00 3.01
307 308 6.946229 ATATTTAGTTCTAGCATTACCGCG 57.054 37.500 0.00 0.00 36.85 6.46
308 309 2.787601 TAGTTCTAGCATTACCGCGG 57.212 50.000 26.86 26.86 36.85 6.46
339 341 6.541934 AACACCTAGGGAAGTATAGAACAC 57.458 41.667 14.81 0.00 0.00 3.32
351 353 7.491372 GGAAGTATAGAACACAATCGACATGAA 59.509 37.037 0.00 0.00 0.00 2.57
360 362 2.556189 CAATCGACATGAACCACCCAAA 59.444 45.455 0.00 0.00 0.00 3.28
361 363 2.350057 TCGACATGAACCACCCAAAA 57.650 45.000 0.00 0.00 0.00 2.44
441 446 6.080969 TGCAGGTTTATATTTTGGACCCTA 57.919 37.500 0.00 0.00 0.00 3.53
454 459 4.546829 TGGACCCTAATAAGTGTCACAC 57.453 45.455 0.00 0.00 34.10 3.82
474 479 1.448985 GTGTGGCACGAATACATGGT 58.551 50.000 13.77 0.00 0.00 3.55
494 499 4.872691 TGGTAACTCCAAACGTTTTTACGA 59.127 37.500 11.66 11.61 44.12 3.43
511 516 7.773864 TTTTACGACAAGTTTAGTGATGTGA 57.226 32.000 0.00 0.00 0.00 3.58
517 522 6.366061 CGACAAGTTTAGTGATGTGAGAATGA 59.634 38.462 0.00 0.00 0.00 2.57
560 565 6.677781 TGACAACTTTCTTTTCGAATGACT 57.322 33.333 0.00 0.00 32.67 3.41
565 570 8.336080 ACAACTTTCTTTTCGAATGACTAGTTC 58.664 33.333 16.54 0.00 32.67 3.01
569 574 6.780706 TCTTTTCGAATGACTAGTTCCAAC 57.219 37.500 0.00 0.00 0.00 3.77
654 659 1.009675 GCTTCAAGCCACACGTGTG 60.010 57.895 36.13 36.13 45.23 3.82
655 660 1.714899 GCTTCAAGCCACACGTGTGT 61.715 55.000 38.40 23.93 46.17 3.72
669 674 5.050431 CACACGTGTGTCACTTATCATTTGA 60.050 40.000 35.03 0.00 42.83 2.69
700 705 9.918630 ATTTTCTGTTATTTCTGATGTTCCTTG 57.081 29.630 0.00 0.00 0.00 3.61
706 711 5.886960 ATTTCTGATGTTCCTTGTACTGC 57.113 39.130 0.00 0.00 0.00 4.40
707 712 4.350368 TTCTGATGTTCCTTGTACTGCA 57.650 40.909 0.00 0.00 0.00 4.41
708 713 4.558226 TCTGATGTTCCTTGTACTGCAT 57.442 40.909 0.00 0.00 0.00 3.96
709 714 4.256110 TCTGATGTTCCTTGTACTGCATG 58.744 43.478 0.00 0.00 0.00 4.06
710 715 4.020307 TCTGATGTTCCTTGTACTGCATGA 60.020 41.667 0.00 0.00 0.00 3.07
711 716 4.847198 TGATGTTCCTTGTACTGCATGAT 58.153 39.130 0.00 0.00 0.00 2.45
712 717 5.988287 TGATGTTCCTTGTACTGCATGATA 58.012 37.500 0.00 0.00 0.00 2.15
713 718 6.594744 TGATGTTCCTTGTACTGCATGATAT 58.405 36.000 0.00 0.00 0.00 1.63
715 720 7.657354 TGATGTTCCTTGTACTGCATGATATAC 59.343 37.037 0.00 0.00 0.00 1.47
852 902 0.454196 GTCCACCACGCACAAAAGTT 59.546 50.000 0.00 0.00 0.00 2.66
853 903 1.135228 GTCCACCACGCACAAAAGTTT 60.135 47.619 0.00 0.00 0.00 2.66
854 904 1.546476 TCCACCACGCACAAAAGTTTT 59.454 42.857 0.00 0.00 0.00 2.43
890 940 5.105554 ACAACCAAGCACAAAAGTACATTGA 60.106 36.000 15.74 0.00 0.00 2.57
893 943 6.402222 ACCAAGCACAAAAGTACATTGAAAA 58.598 32.000 15.74 0.00 0.00 2.29
902 952 4.010667 AGTACATTGAAAAGCCGGTACA 57.989 40.909 1.90 0.00 34.93 2.90
925 975 2.501610 GCCGGCCTGTTCCTCTAG 59.498 66.667 18.11 0.00 0.00 2.43
935 985 1.677966 TTCCTCTAGCCGTGCTCGT 60.678 57.895 7.47 0.00 40.44 4.18
1016 1066 4.587189 CGAAGCCCCCGTCCGATC 62.587 72.222 0.00 0.00 0.00 3.69
1317 1379 2.520741 GGAGGCGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1318 1380 2.520741 GAGGCGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
1319 1381 3.024356 AGGCGAGGAGGAGGAGGA 61.024 66.667 0.00 0.00 0.00 3.71
1754 1816 9.150348 GATGTGAATTATTTTGTTTTACCTGGG 57.850 33.333 0.00 0.00 0.00 4.45
1901 1988 1.909376 TTGACACGATTAGCTCTCGC 58.091 50.000 16.14 3.91 39.71 5.03
1931 2019 8.911247 ATCTTATTCTTCAAATTTGTAACGCC 57.089 30.769 17.47 0.00 0.00 5.68
1933 2021 3.546002 TCTTCAAATTTGTAACGCCGG 57.454 42.857 17.47 0.00 0.00 6.13
2014 2102 3.707316 ACTGAGTGAGCACTAATCTCCT 58.293 45.455 2.65 0.00 42.66 3.69
2015 2103 3.699038 ACTGAGTGAGCACTAATCTCCTC 59.301 47.826 2.65 0.00 42.66 3.71
2016 2104 3.027412 TGAGTGAGCACTAATCTCCTCC 58.973 50.000 2.65 0.00 42.66 4.30
2072 2160 5.882557 GGAGAGATTTGCCACTCTTATTTGA 59.117 40.000 0.00 0.00 42.51 2.69
2075 2163 6.944862 AGAGATTTGCCACTCTTATTTGACTT 59.055 34.615 0.00 0.00 40.02 3.01
2078 2166 5.689383 TTGCCACTCTTATTTGACTTGTC 57.311 39.130 0.00 0.00 0.00 3.18
2084 2228 7.064016 GCCACTCTTATTTGACTTGTCTTAGAG 59.936 40.741 2.35 0.00 34.33 2.43
2180 2325 0.743345 GGCTGTCCATACCGTGTTCC 60.743 60.000 0.00 0.00 0.00 3.62
2221 2366 1.319614 GCCGGCCTCATTTTGCCTTA 61.320 55.000 18.11 0.00 45.71 2.69
2237 2382 6.398234 TTGCCTTACAACAGCAAGAATTTA 57.602 33.333 0.00 0.00 41.35 1.40
2257 2402 9.422196 GAATTTACTGACACAGTTATAAATCGC 57.578 33.333 9.63 3.85 42.59 4.58
2258 2403 6.897259 TTACTGACACAGTTATAAATCGCC 57.103 37.500 9.63 0.00 42.59 5.54
2259 2404 4.827692 ACTGACACAGTTATAAATCGCCA 58.172 39.130 0.00 0.00 42.59 5.69
2260 2405 5.428253 ACTGACACAGTTATAAATCGCCAT 58.572 37.500 0.00 0.00 42.59 4.40
2261 2406 5.880332 ACTGACACAGTTATAAATCGCCATT 59.120 36.000 0.00 0.00 42.59 3.16
2262 2407 6.374333 ACTGACACAGTTATAAATCGCCATTT 59.626 34.615 0.00 0.00 42.59 2.32
2263 2408 6.781138 TGACACAGTTATAAATCGCCATTTC 58.219 36.000 0.00 0.00 33.95 2.17
2264 2409 6.372937 TGACACAGTTATAAATCGCCATTTCA 59.627 34.615 0.00 0.00 33.95 2.69
2265 2410 7.066887 TGACACAGTTATAAATCGCCATTTCAT 59.933 33.333 0.00 0.00 33.95 2.57
2266 2411 7.417612 ACACAGTTATAAATCGCCATTTCATC 58.582 34.615 0.00 0.00 33.95 2.92
2267 2412 6.574832 CACAGTTATAAATCGCCATTTCATCG 59.425 38.462 0.00 0.00 33.95 3.84
2268 2413 6.481976 ACAGTTATAAATCGCCATTTCATCGA 59.518 34.615 0.00 0.00 33.95 3.59
2269 2414 6.792250 CAGTTATAAATCGCCATTTCATCGAC 59.208 38.462 0.00 0.00 33.95 4.20
2270 2415 6.481976 AGTTATAAATCGCCATTTCATCGACA 59.518 34.615 0.00 0.00 33.95 4.35
2271 2416 3.405170 AAATCGCCATTTCATCGACAC 57.595 42.857 0.00 0.00 34.92 3.67
2272 2417 2.315925 ATCGCCATTTCATCGACACT 57.684 45.000 0.00 0.00 34.92 3.55
2273 2418 1.358877 TCGCCATTTCATCGACACTG 58.641 50.000 0.00 0.00 0.00 3.66
2274 2419 0.247814 CGCCATTTCATCGACACTGC 60.248 55.000 0.00 0.00 0.00 4.40
2275 2420 1.089920 GCCATTTCATCGACACTGCT 58.910 50.000 0.00 0.00 0.00 4.24
2292 2437 0.543749 GCTGGTGTTAGGGCATCTCT 59.456 55.000 0.00 0.00 0.00 3.10
2363 2510 2.687566 CTAGTTCGGCCCCTGGGT 60.688 66.667 12.71 0.00 37.65 4.51
2364 2511 2.686106 TAGTTCGGCCCCTGGGTC 60.686 66.667 12.71 0.00 37.65 4.46
2436 2590 1.218316 GGTCGTTCCCGCTCTCAAT 59.782 57.895 0.00 0.00 0.00 2.57
2529 2683 0.673333 TGCGCAATGATTCACTCGGT 60.673 50.000 8.16 0.00 0.00 4.69
2739 2893 3.204827 GATGAGGCCGCGTTGCAT 61.205 61.111 4.92 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.656998 TGCTTCGGCGCAAATTCAA 59.343 47.368 10.83 0.00 45.37 2.69
12 13 3.964221 TAGTCTGCGTGCTTCGGCG 62.964 63.158 0.00 0.00 45.37 6.46
13 14 1.519455 ATAGTCTGCGTGCTTCGGC 60.519 57.895 4.36 0.00 40.26 5.54
14 15 1.148157 CCATAGTCTGCGTGCTTCGG 61.148 60.000 4.36 0.00 40.26 4.30
15 16 1.148157 CCCATAGTCTGCGTGCTTCG 61.148 60.000 0.00 0.00 43.12 3.79
16 17 1.432270 GCCCATAGTCTGCGTGCTTC 61.432 60.000 0.00 0.00 0.00 3.86
17 18 1.450312 GCCCATAGTCTGCGTGCTT 60.450 57.895 0.00 0.00 0.00 3.91
18 19 2.187946 GCCCATAGTCTGCGTGCT 59.812 61.111 0.00 0.00 0.00 4.40
19 20 2.897350 GGCCCATAGTCTGCGTGC 60.897 66.667 0.00 0.00 0.00 5.34
20 21 2.572095 TTCGGCCCATAGTCTGCGTG 62.572 60.000 0.00 0.00 0.00 5.34
21 22 1.895020 TTTCGGCCCATAGTCTGCGT 61.895 55.000 0.00 0.00 0.00 5.24
22 23 0.532862 ATTTCGGCCCATAGTCTGCG 60.533 55.000 0.00 0.00 0.00 5.18
23 24 1.334869 CAATTTCGGCCCATAGTCTGC 59.665 52.381 0.00 0.00 0.00 4.26
24 25 1.949525 CCAATTTCGGCCCATAGTCTG 59.050 52.381 0.00 0.00 0.00 3.51
25 26 1.564348 ACCAATTTCGGCCCATAGTCT 59.436 47.619 0.00 0.00 0.00 3.24
26 27 1.947456 GACCAATTTCGGCCCATAGTC 59.053 52.381 0.00 0.00 0.00 2.59
27 28 1.283613 TGACCAATTTCGGCCCATAGT 59.716 47.619 0.00 0.00 0.00 2.12
28 29 2.051334 TGACCAATTTCGGCCCATAG 57.949 50.000 0.00 0.00 0.00 2.23
29 30 2.516227 TTGACCAATTTCGGCCCATA 57.484 45.000 0.00 0.00 0.00 2.74
30 31 1.864669 ATTGACCAATTTCGGCCCAT 58.135 45.000 0.00 0.00 0.00 4.00
31 32 1.638529 AATTGACCAATTTCGGCCCA 58.361 45.000 0.00 0.00 37.74 5.36
32 33 2.345876 CAAATTGACCAATTTCGGCCC 58.654 47.619 15.47 0.00 46.01 5.80
33 34 1.731709 GCAAATTGACCAATTTCGGCC 59.268 47.619 15.47 0.00 46.01 6.13
34 35 2.411904 TGCAAATTGACCAATTTCGGC 58.588 42.857 15.47 16.25 46.01 5.54
35 36 3.304026 CGATGCAAATTGACCAATTTCGG 59.696 43.478 15.47 8.72 46.01 4.30
36 37 4.165036 TCGATGCAAATTGACCAATTTCG 58.835 39.130 15.47 15.50 46.01 3.46
37 38 6.974622 ACTATCGATGCAAATTGACCAATTTC 59.025 34.615 15.47 11.72 46.01 2.17
39 40 6.267817 CACTATCGATGCAAATTGACCAATT 58.732 36.000 8.54 2.38 42.35 2.32
40 41 5.221106 CCACTATCGATGCAAATTGACCAAT 60.221 40.000 8.54 0.00 0.00 3.16
41 42 4.096231 CCACTATCGATGCAAATTGACCAA 59.904 41.667 8.54 0.00 0.00 3.67
42 43 3.627123 CCACTATCGATGCAAATTGACCA 59.373 43.478 8.54 0.00 0.00 4.02
43 44 3.003689 CCCACTATCGATGCAAATTGACC 59.996 47.826 8.54 0.00 0.00 4.02
44 45 3.548818 GCCCACTATCGATGCAAATTGAC 60.549 47.826 8.54 0.00 0.00 3.18
45 46 2.618241 GCCCACTATCGATGCAAATTGA 59.382 45.455 8.54 0.00 0.00 2.57
46 47 2.287788 GGCCCACTATCGATGCAAATTG 60.288 50.000 8.54 0.00 0.00 2.32
47 48 1.956477 GGCCCACTATCGATGCAAATT 59.044 47.619 8.54 0.00 0.00 1.82
48 49 1.133823 TGGCCCACTATCGATGCAAAT 60.134 47.619 8.54 0.00 0.00 2.32
49 50 0.254462 TGGCCCACTATCGATGCAAA 59.746 50.000 8.54 0.00 0.00 3.68
50 51 0.254462 TTGGCCCACTATCGATGCAA 59.746 50.000 8.54 0.00 0.00 4.08
51 52 0.473755 ATTGGCCCACTATCGATGCA 59.526 50.000 8.54 0.00 0.00 3.96
52 53 1.609208 AATTGGCCCACTATCGATGC 58.391 50.000 8.54 1.70 0.00 3.91
53 54 2.287788 GCAAATTGGCCCACTATCGATG 60.288 50.000 8.54 0.52 0.00 3.84
54 55 1.956477 GCAAATTGGCCCACTATCGAT 59.044 47.619 2.16 2.16 0.00 3.59
55 56 1.388547 GCAAATTGGCCCACTATCGA 58.611 50.000 0.00 0.00 0.00 3.59
56 57 0.029300 CGCAAATTGGCCCACTATCG 59.971 55.000 0.00 0.00 0.00 2.92
57 58 0.249031 GCGCAAATTGGCCCACTATC 60.249 55.000 0.30 0.00 0.00 2.08
58 59 1.675720 GGCGCAAATTGGCCCACTAT 61.676 55.000 10.83 0.00 43.64 2.12
59 60 2.347322 GGCGCAAATTGGCCCACTA 61.347 57.895 10.83 0.00 43.64 2.74
60 61 3.694538 GGCGCAAATTGGCCCACT 61.695 61.111 10.83 0.00 43.64 4.00
63 64 2.010582 TTATCGGCGCAAATTGGCCC 62.011 55.000 10.83 0.73 46.73 5.80
64 65 0.031994 ATTATCGGCGCAAATTGGCC 59.968 50.000 10.83 13.23 45.95 5.36
65 66 2.225491 TCTATTATCGGCGCAAATTGGC 59.775 45.455 10.83 0.00 0.00 4.52
66 67 3.498397 AGTCTATTATCGGCGCAAATTGG 59.502 43.478 10.83 1.87 0.00 3.16
67 68 4.211164 TCAGTCTATTATCGGCGCAAATTG 59.789 41.667 10.83 5.63 0.00 2.32
68 69 4.377021 TCAGTCTATTATCGGCGCAAATT 58.623 39.130 10.83 0.00 0.00 1.82
69 70 3.990092 TCAGTCTATTATCGGCGCAAAT 58.010 40.909 10.83 6.90 0.00 2.32
70 71 3.446310 TCAGTCTATTATCGGCGCAAA 57.554 42.857 10.83 0.00 0.00 3.68
71 72 3.446310 TTCAGTCTATTATCGGCGCAA 57.554 42.857 10.83 0.00 0.00 4.85
72 73 3.446310 TTTCAGTCTATTATCGGCGCA 57.554 42.857 10.83 0.00 0.00 6.09
73 74 3.802685 ACTTTTCAGTCTATTATCGGCGC 59.197 43.478 0.00 0.00 0.00 6.53
74 75 4.209288 CCACTTTTCAGTCTATTATCGGCG 59.791 45.833 0.00 0.00 0.00 6.46
75 76 5.234543 GTCCACTTTTCAGTCTATTATCGGC 59.765 44.000 0.00 0.00 0.00 5.54
76 77 5.753921 GGTCCACTTTTCAGTCTATTATCGG 59.246 44.000 0.00 0.00 0.00 4.18
77 78 6.338146 TGGTCCACTTTTCAGTCTATTATCG 58.662 40.000 0.00 0.00 0.00 2.92
78 79 8.738645 ATTGGTCCACTTTTCAGTCTATTATC 57.261 34.615 0.00 0.00 0.00 1.75
79 80 9.533831 AAATTGGTCCACTTTTCAGTCTATTAT 57.466 29.630 1.43 0.00 0.00 1.28
80 81 8.792633 CAAATTGGTCCACTTTTCAGTCTATTA 58.207 33.333 4.51 0.00 0.00 0.98
81 82 7.661040 CAAATTGGTCCACTTTTCAGTCTATT 58.339 34.615 4.51 0.00 0.00 1.73
82 83 6.294731 GCAAATTGGTCCACTTTTCAGTCTAT 60.295 38.462 4.51 0.00 0.00 1.98
83 84 5.009610 GCAAATTGGTCCACTTTTCAGTCTA 59.990 40.000 4.51 0.00 0.00 2.59
84 85 4.202151 GCAAATTGGTCCACTTTTCAGTCT 60.202 41.667 4.51 0.00 0.00 3.24
85 86 4.051237 GCAAATTGGTCCACTTTTCAGTC 58.949 43.478 4.51 0.00 0.00 3.51
86 87 3.490761 CGCAAATTGGTCCACTTTTCAGT 60.491 43.478 4.51 0.00 0.00 3.41
87 88 3.052036 CGCAAATTGGTCCACTTTTCAG 58.948 45.455 4.51 0.00 0.00 3.02
88 89 2.801342 GCGCAAATTGGTCCACTTTTCA 60.801 45.455 0.30 0.00 0.00 2.69
89 90 1.792367 GCGCAAATTGGTCCACTTTTC 59.208 47.619 0.30 0.00 0.00 2.29
90 91 1.540146 GGCGCAAATTGGTCCACTTTT 60.540 47.619 10.83 0.00 0.00 2.27
91 92 0.033366 GGCGCAAATTGGTCCACTTT 59.967 50.000 10.83 1.43 0.00 2.66
92 93 1.665442 GGCGCAAATTGGTCCACTT 59.335 52.632 10.83 0.00 0.00 3.16
93 94 2.625823 CGGCGCAAATTGGTCCACT 61.626 57.895 10.83 0.00 0.00 4.00
94 95 2.126502 CGGCGCAAATTGGTCCAC 60.127 61.111 10.83 0.00 0.00 4.02
95 96 1.456196 TTTCGGCGCAAATTGGTCCA 61.456 50.000 10.83 0.00 0.00 4.02
96 97 0.732538 CTTTCGGCGCAAATTGGTCC 60.733 55.000 10.83 0.00 0.00 4.46
97 98 0.039527 ACTTTCGGCGCAAATTGGTC 60.040 50.000 10.83 0.00 0.00 4.02
98 99 0.318614 CACTTTCGGCGCAAATTGGT 60.319 50.000 10.83 0.00 0.00 3.67
99 100 1.008361 CCACTTTCGGCGCAAATTGG 61.008 55.000 10.83 18.71 31.80 3.16
100 101 1.008361 CCCACTTTCGGCGCAAATTG 61.008 55.000 10.83 6.66 0.00 2.32
101 102 1.288752 CCCACTTTCGGCGCAAATT 59.711 52.632 10.83 0.00 0.00 1.82
102 103 2.961768 CCCACTTTCGGCGCAAAT 59.038 55.556 10.83 0.00 0.00 2.32
103 104 3.972276 GCCCACTTTCGGCGCAAA 61.972 61.111 10.83 0.33 36.47 3.68
108 109 2.266376 GATTTCGGCCCACTTTCGGC 62.266 60.000 0.00 0.00 46.29 5.54
109 110 1.800681 GATTTCGGCCCACTTTCGG 59.199 57.895 0.00 0.00 0.00 4.30
110 111 1.423845 CGATTTCGGCCCACTTTCG 59.576 57.895 0.00 0.00 35.37 3.46
156 157 2.822701 GGCGATCGGGTTCCCAAC 60.823 66.667 18.30 0.00 0.00 3.77
157 158 4.104183 GGGCGATCGGGTTCCCAA 62.104 66.667 19.95 0.00 38.62 4.12
160 161 4.851179 GTGGGGCGATCGGGTTCC 62.851 72.222 18.30 9.14 0.00 3.62
171 172 2.180769 GAAAAATCGGCGTGGGGC 59.819 61.111 6.85 0.00 42.51 5.80
172 173 1.506262 CTGAAAAATCGGCGTGGGG 59.494 57.895 6.85 0.00 0.00 4.96
173 174 1.154035 GCTGAAAAATCGGCGTGGG 60.154 57.895 6.85 0.00 31.87 4.61
174 175 1.154035 GGCTGAAAAATCGGCGTGG 60.154 57.895 6.85 0.00 42.62 4.94
175 176 0.039617 TTGGCTGAAAAATCGGCGTG 60.040 50.000 6.85 0.00 42.62 5.34
176 177 0.039527 GTTGGCTGAAAAATCGGCGT 60.040 50.000 6.85 0.00 42.62 5.68
177 178 0.039617 TGTTGGCTGAAAAATCGGCG 60.040 50.000 0.00 0.00 42.62 6.46
178 179 1.418373 GTGTTGGCTGAAAAATCGGC 58.582 50.000 1.00 1.00 41.06 5.54
179 180 1.685302 CGTGTTGGCTGAAAAATCGG 58.315 50.000 0.00 0.00 0.00 4.18
180 181 1.052287 GCGTGTTGGCTGAAAAATCG 58.948 50.000 0.00 0.00 0.00 3.34
181 182 1.418373 GGCGTGTTGGCTGAAAAATC 58.582 50.000 0.00 0.00 40.72 2.17
182 183 0.033366 GGGCGTGTTGGCTGAAAAAT 59.967 50.000 0.00 0.00 44.11 1.82
183 184 1.439644 GGGCGTGTTGGCTGAAAAA 59.560 52.632 0.00 0.00 44.11 1.94
184 185 2.494530 GGGGCGTGTTGGCTGAAAA 61.495 57.895 0.00 0.00 44.11 2.29
185 186 2.909965 GGGGCGTGTTGGCTGAAA 60.910 61.111 0.00 0.00 44.11 2.69
186 187 4.966787 GGGGGCGTGTTGGCTGAA 62.967 66.667 0.00 0.00 44.11 3.02
201 202 0.665835 TTAAAATAGCGCCGCATGGG 59.334 50.000 13.36 2.06 39.58 4.00
202 203 1.925946 GCTTAAAATAGCGCCGCATGG 60.926 52.381 13.36 0.00 38.77 3.66
203 204 1.398595 GCTTAAAATAGCGCCGCATG 58.601 50.000 13.36 0.00 0.00 4.06
204 205 3.845625 GCTTAAAATAGCGCCGCAT 57.154 47.368 13.36 0.00 0.00 4.73
211 212 0.668535 CCCCAGGCGCTTAAAATAGC 59.331 55.000 7.64 0.00 37.80 2.97
212 213 0.668535 GCCCCAGGCGCTTAAAATAG 59.331 55.000 7.64 0.00 39.62 1.73
213 214 2.801859 GCCCCAGGCGCTTAAAATA 58.198 52.632 7.64 0.00 39.62 1.40
214 215 3.616086 GCCCCAGGCGCTTAAAAT 58.384 55.556 7.64 0.00 39.62 1.82
231 232 1.372087 GAGCATCTCCAGCCGTTTGG 61.372 60.000 0.00 0.00 39.70 3.28
232 233 2.093216 GAGCATCTCCAGCCGTTTG 58.907 57.895 0.00 0.00 0.00 2.93
233 234 4.625800 GAGCATCTCCAGCCGTTT 57.374 55.556 0.00 0.00 0.00 3.60
244 245 5.355350 AGCCATTGTTACAGTTAAGAGCATC 59.645 40.000 0.00 0.00 0.00 3.91
245 246 5.124457 CAGCCATTGTTACAGTTAAGAGCAT 59.876 40.000 0.00 0.00 0.00 3.79
246 247 4.455533 CAGCCATTGTTACAGTTAAGAGCA 59.544 41.667 0.00 0.00 0.00 4.26
247 248 4.142600 CCAGCCATTGTTACAGTTAAGAGC 60.143 45.833 0.00 0.00 0.00 4.09
248 249 5.245531 TCCAGCCATTGTTACAGTTAAGAG 58.754 41.667 0.00 0.00 0.00 2.85
249 250 5.221843 ACTCCAGCCATTGTTACAGTTAAGA 60.222 40.000 0.00 0.00 0.00 2.10
255 256 2.086869 CCACTCCAGCCATTGTTACAG 58.913 52.381 0.00 0.00 0.00 2.74
262 263 0.767375 ATATCGCCACTCCAGCCATT 59.233 50.000 0.00 0.00 0.00 3.16
263 264 0.322975 GATATCGCCACTCCAGCCAT 59.677 55.000 0.00 0.00 0.00 4.40
285 286 5.009911 TCCGCGGTAATGCTAGAACTAAATA 59.990 40.000 27.15 0.00 0.00 1.40
294 295 1.647346 TTTGTCCGCGGTAATGCTAG 58.353 50.000 27.15 0.00 0.00 3.42
329 331 6.533723 TGGTTCATGTCGATTGTGTTCTATAC 59.466 38.462 0.00 0.00 0.00 1.47
339 341 1.819928 TGGGTGGTTCATGTCGATTG 58.180 50.000 0.00 0.00 0.00 2.67
415 420 5.046950 GGGTCCAAAATATAAACCTGCAACA 60.047 40.000 0.00 0.00 0.00 3.33
417 422 5.337788 AGGGTCCAAAATATAAACCTGCAA 58.662 37.500 0.00 0.00 0.00 4.08
474 479 6.091986 ACTTGTCGTAAAAACGTTTGGAGTTA 59.908 34.615 15.46 6.55 0.00 2.24
492 497 6.366061 TCATTCTCACATCACTAAACTTGTCG 59.634 38.462 0.00 0.00 0.00 4.35
494 499 6.992123 TGTCATTCTCACATCACTAAACTTGT 59.008 34.615 0.00 0.00 0.00 3.16
623 628 2.947243 GCTTGAAGCAATCCCATCCTGA 60.947 50.000 13.09 0.00 41.89 3.86
626 631 0.749049 GGCTTGAAGCAATCCCATCC 59.251 55.000 19.89 0.00 44.75 3.51
636 641 1.009675 CACACGTGTGGCTTGAAGC 60.010 57.895 35.65 9.04 42.10 3.86
679 684 8.446273 CAGTACAAGGAACATCAGAAATAACAG 58.554 37.037 0.00 0.00 0.00 3.16
767 776 9.771534 TTTTTCATTCCATTCTTAATTTTCGGT 57.228 25.926 0.00 0.00 0.00 4.69
795 804 4.052229 CGTGGCGAAGAGGGACGT 62.052 66.667 0.00 0.00 0.00 4.34
863 913 1.289276 CTTTTGTGCTTGGTTGTGCC 58.711 50.000 0.00 0.00 37.90 5.01
864 914 2.008752 ACTTTTGTGCTTGGTTGTGC 57.991 45.000 0.00 0.00 0.00 4.57
865 915 4.103365 TGTACTTTTGTGCTTGGTTGTG 57.897 40.909 0.00 0.00 35.99 3.33
867 917 5.347342 TCAATGTACTTTTGTGCTTGGTTG 58.653 37.500 8.38 0.00 35.99 3.77
870 920 6.509997 GCTTTTCAATGTACTTTTGTGCTTGG 60.510 38.462 8.38 0.00 35.99 3.61
871 921 6.413269 GCTTTTCAATGTACTTTTGTGCTTG 58.587 36.000 8.38 0.00 35.99 4.01
873 923 5.049828 GGCTTTTCAATGTACTTTTGTGCT 58.950 37.500 8.38 0.00 35.99 4.40
874 924 4.085107 CGGCTTTTCAATGTACTTTTGTGC 60.085 41.667 8.38 8.56 35.53 4.57
913 963 1.153549 GCACGGCTAGAGGAACAGG 60.154 63.158 0.00 0.00 0.00 4.00
935 985 1.340991 GGCCTAAACTGATGGGCTTCA 60.341 52.381 0.00 0.00 43.62 3.02
1016 1066 3.313524 GGGGGTTTTGCCTGCTGG 61.314 66.667 5.03 5.03 37.43 4.85
1187 1246 2.257286 CTTTGCCGGTGAATCTGCGG 62.257 60.000 1.90 0.00 0.00 5.69
1188 1247 1.135315 CTTTGCCGGTGAATCTGCG 59.865 57.895 1.90 0.00 0.00 5.18
1189 1248 0.960364 TCCTTTGCCGGTGAATCTGC 60.960 55.000 1.90 0.00 0.00 4.26
1190 1249 1.470098 CTTCCTTTGCCGGTGAATCTG 59.530 52.381 1.90 0.00 0.00 2.90
1191 1250 1.351017 TCTTCCTTTGCCGGTGAATCT 59.649 47.619 1.90 0.00 0.00 2.40
1302 1361 2.581726 CTTCCTCCTCCTCCTCGCCT 62.582 65.000 0.00 0.00 0.00 5.52
1317 1379 2.708593 AAAACCCGCACTCCCCTTCC 62.709 60.000 0.00 0.00 0.00 3.46
1318 1380 1.228459 AAAACCCGCACTCCCCTTC 60.228 57.895 0.00 0.00 0.00 3.46
1319 1381 1.530655 CAAAACCCGCACTCCCCTT 60.531 57.895 0.00 0.00 0.00 3.95
1643 1705 2.482839 GCAAGATCCTCCTTCTCCTTCG 60.483 54.545 0.00 0.00 0.00 3.79
1678 1740 3.628646 AAGATCCCACACCAGCGCC 62.629 63.158 2.29 0.00 0.00 6.53
1681 1743 2.401766 CGCAAGATCCCACACCAGC 61.402 63.158 0.00 0.00 43.02 4.85
1682 1744 1.296392 TCGCAAGATCCCACACCAG 59.704 57.895 0.00 0.00 45.01 4.00
1683 1745 3.477582 TCGCAAGATCCCACACCA 58.522 55.556 0.00 0.00 45.01 4.17
1754 1816 2.401766 CCACCTTGCAGATCACGCC 61.402 63.158 4.85 0.00 0.00 5.68
1901 1988 9.773328 TTACAAATTTGAAGAATAAGATCAGCG 57.227 29.630 24.64 0.00 0.00 5.18
1931 2019 0.306228 TTGTTTGACACGCATGACCG 59.694 50.000 0.00 0.00 0.00 4.79
1933 2021 3.626977 TCAATTGTTTGACACGCATGAC 58.373 40.909 5.13 0.00 36.94 3.06
1943 2031 6.616947 ACGAACTTTCTTGTCAATTGTTTGA 58.383 32.000 5.13 0.00 39.54 2.69
2014 2102 2.851263 AACCAGCATCTAACAACGGA 57.149 45.000 0.00 0.00 0.00 4.69
2015 2103 3.004315 ACAAAACCAGCATCTAACAACGG 59.996 43.478 0.00 0.00 0.00 4.44
2016 2104 4.223320 ACAAAACCAGCATCTAACAACG 57.777 40.909 0.00 0.00 0.00 4.10
2072 2160 4.926238 CGCTGACAAATCTCTAAGACAAGT 59.074 41.667 0.00 0.00 0.00 3.16
2075 2163 4.783764 TCGCTGACAAATCTCTAAGACA 57.216 40.909 0.00 0.00 0.00 3.41
2078 2166 7.521529 TCAAAATTCGCTGACAAATCTCTAAG 58.478 34.615 0.00 0.00 0.00 2.18
2084 2228 4.229096 TGCTCAAAATTCGCTGACAAATC 58.771 39.130 0.00 0.00 0.00 2.17
2180 2325 3.523547 TGGAACCAACATATACCGAACG 58.476 45.455 0.00 0.00 0.00 3.95
2221 2366 5.356751 TGTGTCAGTAAATTCTTGCTGTTGT 59.643 36.000 3.43 0.00 43.54 3.32
2237 2382 6.374333 AAATGGCGATTTATAACTGTGTCAGT 59.626 34.615 4.72 0.00 36.82 3.41
2254 2399 1.358877 CAGTGTCGATGAAATGGCGA 58.641 50.000 0.00 0.00 0.00 5.54
2255 2400 0.247814 GCAGTGTCGATGAAATGGCG 60.248 55.000 0.00 0.00 0.00 5.69
2256 2401 1.089920 AGCAGTGTCGATGAAATGGC 58.910 50.000 0.00 0.00 0.00 4.40
2257 2402 1.399440 CCAGCAGTGTCGATGAAATGG 59.601 52.381 0.00 0.00 0.00 3.16
2258 2403 2.079158 ACCAGCAGTGTCGATGAAATG 58.921 47.619 0.00 0.00 0.00 2.32
2259 2404 2.079158 CACCAGCAGTGTCGATGAAAT 58.921 47.619 0.00 0.00 41.93 2.17
2260 2405 1.511850 CACCAGCAGTGTCGATGAAA 58.488 50.000 0.00 0.00 41.93 2.69
2261 2406 3.215642 CACCAGCAGTGTCGATGAA 57.784 52.632 0.00 0.00 41.93 2.57
2262 2407 4.994744 CACCAGCAGTGTCGATGA 57.005 55.556 0.00 0.00 41.93 2.92
2270 2415 0.035056 GATGCCCTAACACCAGCAGT 60.035 55.000 0.00 0.00 38.89 4.40
2271 2416 0.254178 AGATGCCCTAACACCAGCAG 59.746 55.000 0.00 0.00 38.89 4.24
2272 2417 0.253044 GAGATGCCCTAACACCAGCA 59.747 55.000 0.00 0.00 40.00 4.41
2273 2418 0.543749 AGAGATGCCCTAACACCAGC 59.456 55.000 0.00 0.00 0.00 4.85
2274 2419 3.034635 ACTAGAGATGCCCTAACACCAG 58.965 50.000 0.00 0.00 0.00 4.00
2275 2420 3.031736 GACTAGAGATGCCCTAACACCA 58.968 50.000 0.00 0.00 0.00 4.17
2292 2437 3.072468 CTGGGGGCCGAACGACTA 61.072 66.667 0.00 0.00 0.00 2.59
2436 2590 2.202824 CCGGATTTGCGGCGTCTA 60.203 61.111 9.37 0.00 0.00 2.59
2734 2888 1.376683 GGCGTGGTACCTGATGCAA 60.377 57.895 14.36 0.00 0.00 4.08
2739 2893 1.972198 CTCAAGGCGTGGTACCTGA 59.028 57.895 14.36 6.28 37.67 3.86


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

AutoCloner maintained by Alex Coulton.