Multiple sequence alignment - TraesCS5A01G300300

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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 TraesCS5A01G300300 chr5A 100.000 4513 0 0 1 4513 509648765 509653277 0.000000e+00 8335.0
1 TraesCS5A01G300300 chr5A 85.115 262 28 5 1394 1644 599797910 599798171 1.610000e-64 257.0
2 TraesCS5A01G300300 chr5B 90.438 1485 103 14 2566 4022 485909941 485908468 0.000000e+00 1919.0
3 TraesCS5A01G300300 chr5B 94.915 590 24 2 849 1435 485913460 485912874 0.000000e+00 918.0
4 TraesCS5A01G300300 chr5B 89.379 612 63 2 1958 2567 485912072 485911461 0.000000e+00 769.0
5 TraesCS5A01G300300 chr5B 93.443 366 17 3 1443 1801 485912824 485912459 1.850000e-148 536.0
6 TraesCS5A01G300300 chr5B 93.503 354 18 3 4160 4513 485908233 485907885 5.170000e-144 521.0
7 TraesCS5A01G300300 chr5B 82.895 380 48 13 387 754 485913981 485913607 4.350000e-85 326.0
8 TraesCS5A01G300300 chr5B 94.309 123 7 0 1835 1957 485912459 485912337 5.960000e-44 189.0
9 TraesCS5A01G300300 chr5B 98.913 92 1 0 205 296 485914080 485913989 1.000000e-36 165.0
10 TraesCS5A01G300300 chr5D 92.033 1318 67 13 1443 2756 404502148 404500865 0.000000e+00 1818.0
11 TraesCS5A01G300300 chr5D 88.583 1270 74 27 2776 4022 404499530 404498309 0.000000e+00 1476.0
12 TraesCS5A01G300300 chr5D 94.799 596 21 2 849 1435 404502793 404502199 0.000000e+00 920.0
13 TraesCS5A01G300300 chr5D 87.193 570 50 19 202 754 404503502 404502939 1.070000e-175 627.0
14 TraesCS5A01G300300 chr5D 92.130 216 15 2 4020 4234 404497936 404497722 2.040000e-78 303.0
15 TraesCS5A01G300300 chr5D 90.291 206 16 2 1443 1644 480700062 480700267 2.680000e-67 267.0
16 TraesCS5A01G300300 chr5D 88.835 206 19 2 1443 1644 511472578 511472783 2.700000e-62 250.0
17 TraesCS5A01G300300 chr5D 88.462 208 22 1 4 211 528851938 528851733 2.700000e-62 250.0
18 TraesCS5A01G300300 chr5D 85.385 130 17 1 4 133 501357877 501358004 2.830000e-27 134.0
19 TraesCS5A01G300300 chr7D 84.615 403 50 7 452 843 607213976 607214377 1.520000e-104 390.0
20 TraesCS5A01G300300 chr7D 81.265 411 59 10 451 846 30245332 30244925 2.620000e-82 316.0
21 TraesCS5A01G300300 chr7D 89.855 207 18 3 4 208 501024833 501025038 3.460000e-66 263.0
22 TraesCS5A01G300300 chr7D 89.320 206 18 2 1443 1644 620849530 620849735 5.790000e-64 255.0
23 TraesCS5A01G300300 chr7D 82.011 189 23 4 669 847 56617061 56616874 2.810000e-32 150.0
24 TraesCS5A01G300300 chr2B 82.544 401 50 14 459 843 137261519 137261123 7.230000e-88 335.0
25 TraesCS5A01G300300 chr2B 80.377 265 36 13 3061 3317 10775710 10775454 2.140000e-43 187.0
26 TraesCS5A01G300300 chr2B 81.538 195 31 3 2370 2564 11226609 11226420 6.040000e-34 156.0
27 TraesCS5A01G300300 chr2B 87.302 126 16 0 2438 2563 11173140 11173015 1.310000e-30 145.0
28 TraesCS5A01G300300 chr6B 82.064 407 53 11 453 843 159399469 159399871 3.370000e-86 329.0
29 TraesCS5A01G300300 chr6B 85.517 145 17 2 3882 4022 49615581 49615437 1.010000e-31 148.0
30 TraesCS5A01G300300 chr7B 81.679 393 58 11 459 843 5266355 5265969 9.420000e-82 315.0
31 TraesCS5A01G300300 chr4A 80.976 410 57 11 460 849 16476973 16477381 5.670000e-79 305.0
32 TraesCS5A01G300300 chr7A 93.627 204 12 1 4 207 629017960 629017758 2.040000e-78 303.0
33 TraesCS5A01G300300 chr7A 93.171 205 12 2 4 206 118571695 118571899 2.640000e-77 300.0
34 TraesCS5A01G300300 chr4D 80.732 410 59 13 452 843 15347805 15347398 7.340000e-78 302.0
35 TraesCS5A01G300300 chr2D 93.171 205 12 1 4 206 558187170 558187374 2.640000e-77 300.0
36 TraesCS5A01G300300 chr2D 89.202 213 17 4 1443 1649 42209747 42209535 1.250000e-65 261.0
37 TraesCS5A01G300300 chr2D 84.783 230 19 6 3374 3591 683760 683985 2.730000e-52 217.0
38 TraesCS5A01G300300 chr2D 81.481 216 29 4 2349 2564 8479540 8479336 2.790000e-37 167.0
39 TraesCS5A01G300300 chr3D 92.754 207 13 2 4 208 550555821 550556027 9.490000e-77 298.0
40 TraesCS5A01G300300 chr3D 89.202 213 17 4 1443 1649 26967988 26967776 1.250000e-65 261.0
41 TraesCS5A01G300300 chr6A 92.647 204 13 1 4 205 91908566 91908363 4.420000e-75 292.0
42 TraesCS5A01G300300 chr2A 90.594 202 17 1 4 205 117525676 117525477 2.680000e-67 267.0
43 TraesCS5A01G300300 chr2A 86.207 145 16 2 3882 4022 13031463 13031607 2.170000e-33 154.0
44 TraesCS5A01G300300 chr2A 92.105 38 3 0 4158 4195 536933 536970 2.000000e-03 54.7
45 TraesCS5A01G300300 chr4B 90.594 202 14 3 4 205 165827525 165827721 3.460000e-66 263.0
46 TraesCS5A01G300300 chr6D 80.052 381 53 17 466 833 438157201 438157571 1.250000e-65 261.0
47 TraesCS5A01G300300 chr1D 88.732 213 18 4 1443 1649 31007846 31007634 5.790000e-64 255.0
48 TraesCS5A01G300300 chr1D 85.385 130 17 2 4 133 12289154 12289281 2.830000e-27 134.0
49 TraesCS5A01G300300 chr1A 83.732 209 28 6 4 212 382734863 382735065 4.610000e-45 193.0


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 TraesCS5A01G300300 chr5A 509648765 509653277 4512 False 8335.000 8335 100.000000 1 4513 1 chr5A.!!$F1 4512
1 TraesCS5A01G300300 chr5B 485907885 485914080 6195 True 667.875 1919 92.224375 205 4513 8 chr5B.!!$R1 4308
2 TraesCS5A01G300300 chr5D 404497722 404503502 5780 True 1028.800 1818 90.947600 202 4234 5 chr5D.!!$R2 4032


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
199 200 0.032952 GGCAACACACGGACAGTCTA 59.967 55.0 0.00 0.0 0.00 2.59 F
843 898 0.322546 GGGCACCGAGTTGGATTTCT 60.323 55.0 2.42 0.0 40.86 2.52 F
1231 1318 0.036765 ATTTCTTACCGTCGCTGGCA 60.037 50.0 0.00 0.0 0.00 4.92 F
2087 2489 0.108424 CTCCTGCTTTCTCCACCGAG 60.108 60.0 0.00 0.0 37.48 4.63 F
3351 6602 0.396556 TATCGGCTGTAGTCCTGGCA 60.397 55.0 0.00 0.0 37.41 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 1318 0.389391 CGTATTCACCTGGCGGAGAT 59.611 55.0 0.00 0.0 29.70 2.75 R
2067 2469 0.541998 TCGGTGGAGAAAGCAGGAGA 60.542 55.0 0.00 0.0 0.00 3.71 R
3083 6334 1.162181 CGGCACCATGGCAGTATCAG 61.162 60.0 13.04 0.0 43.94 2.90 R
3500 6751 0.178958 GGGGAGGCTAGAGATTCCGA 60.179 60.0 0.00 0.0 0.00 4.55 R
4188 7843 1.452145 CCCTGGTGTTTGGTCCAACG 61.452 60.0 2.98 0.0 33.06 4.10 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
25 26 7.833285 ATTGTTTGTGTACCACCTTCTTTAT 57.167 32.000 0.00 0.00 32.73 1.40
26 27 7.648039 TTGTTTGTGTACCACCTTCTTTATT 57.352 32.000 0.00 0.00 32.73 1.40
27 28 7.648039 TGTTTGTGTACCACCTTCTTTATTT 57.352 32.000 0.00 0.00 32.73 1.40
28 29 8.068892 TGTTTGTGTACCACCTTCTTTATTTT 57.931 30.769 0.00 0.00 32.73 1.82
29 30 7.976734 TGTTTGTGTACCACCTTCTTTATTTTG 59.023 33.333 0.00 0.00 32.73 2.44
30 31 7.648039 TTGTGTACCACCTTCTTTATTTTGT 57.352 32.000 0.00 0.00 32.73 2.83
31 32 7.033530 TGTGTACCACCTTCTTTATTTTGTG 57.966 36.000 0.00 0.00 32.73 3.33
32 33 5.918576 GTGTACCACCTTCTTTATTTTGTGC 59.081 40.000 0.00 0.00 0.00 4.57
33 34 5.594725 TGTACCACCTTCTTTATTTTGTGCA 59.405 36.000 0.00 0.00 0.00 4.57
34 35 5.806654 ACCACCTTCTTTATTTTGTGCAT 57.193 34.783 0.00 0.00 0.00 3.96
35 36 5.783111 ACCACCTTCTTTATTTTGTGCATC 58.217 37.500 0.00 0.00 0.00 3.91
36 37 5.304101 ACCACCTTCTTTATTTTGTGCATCA 59.696 36.000 0.00 0.00 0.00 3.07
37 38 5.865552 CCACCTTCTTTATTTTGTGCATCAG 59.134 40.000 0.00 0.00 0.00 2.90
38 39 5.865552 CACCTTCTTTATTTTGTGCATCAGG 59.134 40.000 0.00 0.00 0.00 3.86
39 40 5.539955 ACCTTCTTTATTTTGTGCATCAGGT 59.460 36.000 0.00 0.00 0.00 4.00
40 41 5.865552 CCTTCTTTATTTTGTGCATCAGGTG 59.134 40.000 0.00 0.00 0.00 4.00
41 42 6.403866 TTCTTTATTTTGTGCATCAGGTGT 57.596 33.333 0.00 0.00 0.00 4.16
42 43 7.309133 CCTTCTTTATTTTGTGCATCAGGTGTA 60.309 37.037 0.00 0.00 0.00 2.90
43 44 7.701539 TCTTTATTTTGTGCATCAGGTGTAT 57.298 32.000 0.00 0.00 0.00 2.29
44 45 8.800370 TCTTTATTTTGTGCATCAGGTGTATA 57.200 30.769 0.00 0.00 0.00 1.47
45 46 8.892723 TCTTTATTTTGTGCATCAGGTGTATAG 58.107 33.333 0.00 0.00 0.00 1.31
46 47 7.566760 TTATTTTGTGCATCAGGTGTATAGG 57.433 36.000 0.00 0.00 0.00 2.57
47 48 3.558931 TTGTGCATCAGGTGTATAGGG 57.441 47.619 0.00 0.00 0.00 3.53
48 49 2.477245 TGTGCATCAGGTGTATAGGGT 58.523 47.619 0.00 0.00 0.00 4.34
49 50 2.434336 TGTGCATCAGGTGTATAGGGTC 59.566 50.000 0.00 0.00 0.00 4.46
50 51 1.686587 TGCATCAGGTGTATAGGGTCG 59.313 52.381 0.00 0.00 0.00 4.79
51 52 1.961394 GCATCAGGTGTATAGGGTCGA 59.039 52.381 0.00 0.00 0.00 4.20
52 53 2.364324 GCATCAGGTGTATAGGGTCGAA 59.636 50.000 0.00 0.00 0.00 3.71
53 54 3.006967 GCATCAGGTGTATAGGGTCGAAT 59.993 47.826 0.00 0.00 0.00 3.34
54 55 4.503296 GCATCAGGTGTATAGGGTCGAATT 60.503 45.833 0.00 0.00 0.00 2.17
55 56 5.279306 GCATCAGGTGTATAGGGTCGAATTA 60.279 44.000 0.00 0.00 0.00 1.40
56 57 6.574465 GCATCAGGTGTATAGGGTCGAATTAT 60.574 42.308 0.00 0.00 0.00 1.28
57 58 7.363530 GCATCAGGTGTATAGGGTCGAATTATA 60.364 40.741 0.00 0.00 0.00 0.98
58 59 8.528643 CATCAGGTGTATAGGGTCGAATTATAA 58.471 37.037 0.00 0.00 0.00 0.98
59 60 8.481492 TCAGGTGTATAGGGTCGAATTATAAA 57.519 34.615 0.00 0.00 0.00 1.40
60 61 8.926374 TCAGGTGTATAGGGTCGAATTATAAAA 58.074 33.333 0.00 0.00 0.00 1.52
61 62 9.550406 CAGGTGTATAGGGTCGAATTATAAAAA 57.450 33.333 0.00 0.00 0.00 1.94
84 85 7.740519 AAAAATATCGAAGTACATTGCAAGC 57.259 32.000 4.94 0.00 0.00 4.01
85 86 4.715520 ATATCGAAGTACATTGCAAGCG 57.284 40.909 4.94 0.64 0.00 4.68
86 87 2.073117 TCGAAGTACATTGCAAGCGA 57.927 45.000 4.94 2.67 0.00 4.93
87 88 2.409012 TCGAAGTACATTGCAAGCGAA 58.591 42.857 4.94 0.00 0.00 4.70
88 89 3.000041 TCGAAGTACATTGCAAGCGAAT 59.000 40.909 4.94 0.00 0.00 3.34
89 90 3.435327 TCGAAGTACATTGCAAGCGAATT 59.565 39.130 4.94 0.00 0.00 2.17
90 91 4.627900 TCGAAGTACATTGCAAGCGAATTA 59.372 37.500 4.94 0.00 0.00 1.40
91 92 4.957967 CGAAGTACATTGCAAGCGAATTAG 59.042 41.667 4.94 0.00 0.00 1.73
92 93 5.220397 CGAAGTACATTGCAAGCGAATTAGA 60.220 40.000 4.94 0.00 0.00 2.10
93 94 6.510157 CGAAGTACATTGCAAGCGAATTAGAT 60.510 38.462 4.94 0.00 0.00 1.98
94 95 6.683974 AGTACATTGCAAGCGAATTAGATT 57.316 33.333 4.94 0.00 0.00 2.40
95 96 6.719365 AGTACATTGCAAGCGAATTAGATTC 58.281 36.000 4.94 0.00 35.94 2.52
96 97 4.925068 ACATTGCAAGCGAATTAGATTCC 58.075 39.130 4.94 0.00 35.89 3.01
97 98 4.398988 ACATTGCAAGCGAATTAGATTCCA 59.601 37.500 4.94 0.00 35.89 3.53
98 99 5.105797 ACATTGCAAGCGAATTAGATTCCAA 60.106 36.000 4.94 0.00 35.89 3.53
99 100 5.581126 TTGCAAGCGAATTAGATTCCAAT 57.419 34.783 0.00 0.00 35.89 3.16
100 101 5.581126 TGCAAGCGAATTAGATTCCAATT 57.419 34.783 0.00 0.00 35.89 2.32
101 102 6.691754 TGCAAGCGAATTAGATTCCAATTA 57.308 33.333 0.00 0.00 35.89 1.40
102 103 6.494842 TGCAAGCGAATTAGATTCCAATTAC 58.505 36.000 0.00 0.00 35.89 1.89
103 104 6.318648 TGCAAGCGAATTAGATTCCAATTACT 59.681 34.615 0.00 0.00 35.89 2.24
104 105 7.148086 TGCAAGCGAATTAGATTCCAATTACTT 60.148 33.333 0.00 0.00 35.89 2.24
105 106 7.702348 GCAAGCGAATTAGATTCCAATTACTTT 59.298 33.333 0.00 0.00 35.89 2.66
106 107 9.573133 CAAGCGAATTAGATTCCAATTACTTTT 57.427 29.630 0.00 0.00 35.89 2.27
136 137 9.461312 TTTGTTATTGCCTATCTTTCTATGTGT 57.539 29.630 0.00 0.00 0.00 3.72
137 138 8.437360 TGTTATTGCCTATCTTTCTATGTGTG 57.563 34.615 0.00 0.00 0.00 3.82
138 139 8.046708 TGTTATTGCCTATCTTTCTATGTGTGT 58.953 33.333 0.00 0.00 0.00 3.72
139 140 9.542462 GTTATTGCCTATCTTTCTATGTGTGTA 57.458 33.333 0.00 0.00 0.00 2.90
142 143 8.856153 TTGCCTATCTTTCTATGTGTGTAAAA 57.144 30.769 0.00 0.00 0.00 1.52
143 144 9.461312 TTGCCTATCTTTCTATGTGTGTAAAAT 57.539 29.630 0.00 0.00 0.00 1.82
144 145 9.461312 TGCCTATCTTTCTATGTGTGTAAAATT 57.539 29.630 0.00 0.00 0.00 1.82
175 176 8.557869 TGCAACAAATACAAATTTTCAAATGC 57.442 26.923 0.00 0.00 32.87 3.56
176 177 7.646922 TGCAACAAATACAAATTTTCAAATGCC 59.353 29.630 0.00 0.00 32.87 4.40
177 178 7.114670 GCAACAAATACAAATTTTCAAATGCCC 59.885 33.333 0.00 0.00 32.87 5.36
178 179 6.896969 ACAAATACAAATTTTCAAATGCCCG 58.103 32.000 0.00 0.00 32.87 6.13
179 180 6.484977 ACAAATACAAATTTTCAAATGCCCGT 59.515 30.769 0.00 0.00 32.87 5.28
180 181 6.479095 AATACAAATTTTCAAATGCCCGTG 57.521 33.333 0.00 0.00 0.00 4.94
181 182 3.137533 ACAAATTTTCAAATGCCCGTGG 58.862 40.909 0.00 0.00 0.00 4.94
182 183 9.377928 AAATACAAATTTTCAAATGCCCGTGGC 62.378 37.037 7.87 7.87 39.65 5.01
196 197 2.587340 TGGCAACACACGGACAGT 59.413 55.556 0.00 0.00 46.17 3.55
197 198 1.522806 TGGCAACACACGGACAGTC 60.523 57.895 0.00 0.00 46.17 3.51
198 199 1.227556 GGCAACACACGGACAGTCT 60.228 57.895 0.00 0.00 0.00 3.24
199 200 0.032952 GGCAACACACGGACAGTCTA 59.967 55.000 0.00 0.00 0.00 2.59
200 201 1.137513 GCAACACACGGACAGTCTAC 58.862 55.000 0.00 0.00 0.00 2.59
296 297 6.177610 TGACCATTCACATTAGTTAACTCCC 58.822 40.000 12.39 0.00 0.00 4.30
299 300 7.182060 ACCATTCACATTAGTTAACTCCCAAT 58.818 34.615 12.39 3.78 0.00 3.16
382 387 2.553079 TTTCCACACGAAACAGTTGC 57.447 45.000 0.00 0.00 35.49 4.17
385 390 1.400142 TCCACACGAAACAGTTGCAAG 59.600 47.619 0.00 0.00 0.00 4.01
388 394 3.497118 CACACGAAACAGTTGCAAGAAA 58.503 40.909 0.00 0.00 0.00 2.52
457 468 0.481128 ACGGAGGGGTTTTTGGATGT 59.519 50.000 0.00 0.00 0.00 3.06
486 497 1.227205 CTCCCGAGCTCATCTGCAC 60.227 63.158 15.40 0.00 34.99 4.57
487 498 1.674764 CTCCCGAGCTCATCTGCACT 61.675 60.000 15.40 0.00 34.99 4.40
489 500 1.674764 CCCGAGCTCATCTGCACTCT 61.675 60.000 15.40 0.00 34.99 3.24
491 502 0.591994 CGAGCTCATCTGCACTCTCG 60.592 60.000 15.40 0.00 37.65 4.04
570 587 5.474532 TGGTAGATAATTTGATGCATGAGGC 59.525 40.000 2.46 0.00 45.13 4.70
584 601 1.337118 TGAGGCCCGCTTCAAATTTT 58.663 45.000 0.00 0.00 0.00 1.82
587 604 3.250744 GAGGCCCGCTTCAAATTTTAAC 58.749 45.455 0.00 0.00 0.00 2.01
589 606 3.323691 AGGCCCGCTTCAAATTTTAACTT 59.676 39.130 0.00 0.00 0.00 2.66
595 612 7.623297 GCCCGCTTCAAATTTTAACTTATTTGG 60.623 37.037 13.02 0.00 40.46 3.28
608 625 6.380079 AACTTATTTGGACATCTGAGGAGT 57.620 37.500 0.00 0.00 0.00 3.85
673 691 0.464036 TTCACGCACTGTTCTGACCT 59.536 50.000 0.00 0.00 0.00 3.85
679 697 3.244078 ACGCACTGTTCTGACCTGATTTA 60.244 43.478 0.00 0.00 0.00 1.40
681 699 4.033358 CGCACTGTTCTGACCTGATTTATC 59.967 45.833 0.00 0.00 0.00 1.75
739 758 2.151202 GAAATTGAAGCGGACCTCACA 58.849 47.619 0.00 0.00 0.00 3.58
741 760 0.670546 ATTGAAGCGGACCTCACACG 60.671 55.000 0.00 0.00 0.00 4.49
750 769 3.259064 CGGACCTCACACGTCAAATTAT 58.741 45.455 0.00 0.00 31.55 1.28
754 773 6.103997 GGACCTCACACGTCAAATTATCTAA 58.896 40.000 0.00 0.00 31.55 2.10
755 774 6.592607 GGACCTCACACGTCAAATTATCTAAA 59.407 38.462 0.00 0.00 31.55 1.85
757 776 8.385898 ACCTCACACGTCAAATTATCTAAAAA 57.614 30.769 0.00 0.00 0.00 1.94
843 898 0.322546 GGGCACCGAGTTGGATTTCT 60.323 55.000 2.42 0.00 40.86 2.52
847 902 1.064825 ACCGAGTTGGATTTCTGGGT 58.935 50.000 2.42 0.00 42.00 4.51
1093 1180 1.642037 CGTCTCCGACCGCTACTTCA 61.642 60.000 0.00 0.00 35.63 3.02
1159 1246 2.267961 GGACAGGTAAGCCCCACG 59.732 66.667 0.00 0.00 34.57 4.94
1170 1257 2.760385 CCCCACGTCTCCCCTCTC 60.760 72.222 0.00 0.00 0.00 3.20
1175 1262 4.824515 CGTCTCCCCTCTCCGCCT 62.825 72.222 0.00 0.00 0.00 5.52
1195 1282 4.572571 GGGCCACGGACACAACCA 62.573 66.667 4.39 0.00 0.00 3.67
1207 1294 0.804989 CACAACCAGCCGGATTCTTC 59.195 55.000 5.05 0.00 35.59 2.87
1231 1318 0.036765 ATTTCTTACCGTCGCTGGCA 60.037 50.000 0.00 0.00 0.00 4.92
1374 1461 2.032528 CTGCTTCCAGGGCGTTCA 59.967 61.111 0.00 0.00 35.38 3.18
1375 1462 1.600636 CTGCTTCCAGGGCGTTCAA 60.601 57.895 0.00 0.00 35.38 2.69
1446 1566 1.608055 TGATTCTTGGTGCTGGTGTG 58.392 50.000 0.00 0.00 0.00 3.82
1447 1567 0.242017 GATTCTTGGTGCTGGTGTGC 59.758 55.000 0.00 0.00 0.00 4.57
1463 1593 4.830765 GCATGCAGGACGCCGGTA 62.831 66.667 14.21 0.00 41.33 4.02
1608 1738 1.806568 GTCAGCCAGGACTCGAGAG 59.193 63.158 21.68 5.72 34.92 3.20
1613 1743 0.825840 GCCAGGACTCGAGAGCCTAT 60.826 60.000 24.14 7.80 34.65 2.57
1659 1793 6.671779 TGCTCCCTTGAATTTACCCATATTTT 59.328 34.615 0.00 0.00 0.00 1.82
1661 1795 6.883744 TCCCTTGAATTTACCCATATTTTGC 58.116 36.000 0.00 0.00 0.00 3.68
1675 1812 5.967674 CCATATTTTGCGTCTTGCTAGAAAG 59.032 40.000 3.78 3.78 46.63 2.62
1680 1817 3.515630 TGCGTCTTGCTAGAAAGATCTG 58.484 45.455 16.47 10.49 46.63 2.90
1792 1929 3.007635 TGTATTGCGAAGAGTCTCTCGA 58.992 45.455 21.26 8.07 35.36 4.04
1801 1939 4.147306 CGAAGAGTCTCTCGAAAACTTGTG 59.853 45.833 15.35 0.00 35.36 3.33
1807 1945 2.549754 CTCTCGAAAACTTGTGTGGCAT 59.450 45.455 0.00 0.00 0.00 4.40
1833 1971 4.390297 GCCACTGAATTTGTACTGAGAGAC 59.610 45.833 0.00 0.00 0.00 3.36
1848 1986 6.234177 ACTGAGAGACTTGTTTCAAATAGGG 58.766 40.000 0.00 0.00 0.00 3.53
1895 2033 7.520798 ACTATGAAGAATGCATTGGATTAGGA 58.479 34.615 18.59 0.00 34.81 2.94
1950 2088 3.650942 ACTGGTTACATGTCCTCTGGAAA 59.349 43.478 0.00 0.00 31.38 3.13
1999 2401 9.880064 CTTGCATATCAAAGTGAATATCAAGAG 57.120 33.333 0.00 0.00 33.65 2.85
2019 2421 9.042450 TCAAGAGGATTTAAGTATGGAGTTGTA 57.958 33.333 0.00 0.00 0.00 2.41
2051 2453 1.075482 CTGGCCAAGAAAGAGCCCA 59.925 57.895 7.01 0.00 46.55 5.36
2063 2465 1.041447 AGAGCCCATTGCCAATGAGC 61.041 55.000 18.84 17.02 42.28 4.26
2067 2469 1.327690 CCCATTGCCAATGAGCTGCT 61.328 55.000 18.84 0.00 41.46 4.24
2069 2471 1.103803 CATTGCCAATGAGCTGCTCT 58.896 50.000 28.04 12.64 41.46 4.09
2087 2489 0.108424 CTCCTGCTTTCTCCACCGAG 60.108 60.000 0.00 0.00 37.48 4.63
2115 2517 5.443230 TCTGGAAAACCCCAAACAATTTT 57.557 34.783 0.00 0.00 35.47 1.82
2142 2544 4.319839 GGTCAAACTTTGCTAGAACAGAGC 60.320 45.833 0.00 0.00 40.53 4.09
2155 2557 6.019479 GCTAGAACAGAGCACACATATGTAAC 60.019 42.308 8.32 0.92 39.84 2.50
2164 2566 6.160684 AGCACACATATGTAACGTGTAGAAA 58.839 36.000 20.01 0.00 41.79 2.52
2177 2579 4.238514 CGTGTAGAAAGAGTCCAAGGAAG 58.761 47.826 0.00 0.00 0.00 3.46
2200 2602 4.065423 ACACGTGCAAAGATAATTGACG 57.935 40.909 17.22 0.00 38.54 4.35
2287 2689 2.674796 AAGAGTCCAACGGCAGATAC 57.325 50.000 0.00 0.00 0.00 2.24
2324 2727 9.830294 AACTAGCAACAATTAATTACCGTTAAC 57.170 29.630 0.00 0.00 0.00 2.01
2388 2791 4.370917 GCTTGTCCATGTCACATGTTTTT 58.629 39.130 16.74 0.00 0.00 1.94
2390 2793 6.158598 GCTTGTCCATGTCACATGTTTTTAT 58.841 36.000 16.74 0.00 0.00 1.40
2598 4524 0.603569 ACAAGTCGTGCTCTGGGTAG 59.396 55.000 0.00 0.00 0.00 3.18
2667 4593 7.867403 GCCAATCTAATTTTGTTTGAGAACTCA 59.133 33.333 0.00 0.00 36.70 3.41
2680 4606 8.988934 TGTTTGAGAACTCATGTAATGTAAGTC 58.011 33.333 5.34 0.00 39.64 3.01
2681 4607 8.443937 GTTTGAGAACTCATGTAATGTAAGTCC 58.556 37.037 5.34 0.00 46.80 3.85
2730 4656 6.071221 ACAGATGTGTTTGCATGGACATAAAT 60.071 34.615 5.29 0.00 30.30 1.40
2773 6022 6.657836 ACACCATTCAGCTAAACGTATTAC 57.342 37.500 0.00 0.00 0.00 1.89
2777 6026 5.978919 CCATTCAGCTAAACGTATTACGGTA 59.021 40.000 19.51 10.49 42.91 4.02
2778 6027 6.643770 CCATTCAGCTAAACGTATTACGGTAT 59.356 38.462 19.51 8.21 42.91 2.73
2779 6028 7.170320 CCATTCAGCTAAACGTATTACGGTATT 59.830 37.037 19.51 13.27 42.91 1.89
2780 6029 9.184062 CATTCAGCTAAACGTATTACGGTATTA 57.816 33.333 19.51 13.62 42.91 0.98
2790 6039 6.783162 CGTATTACGGTATTAGAGATCCCAG 58.217 44.000 8.36 0.00 38.08 4.45
2886 6135 1.202722 CCCATTACGGTTCGGGCTTAT 60.203 52.381 0.00 0.00 0.00 1.73
2891 6140 0.466543 ACGGTTCGGGCTTATGCATA 59.533 50.000 1.16 1.16 41.91 3.14
2911 6160 3.616956 AGAATCGAGCCAACATGAAGA 57.383 42.857 0.00 0.00 0.00 2.87
2919 6168 1.363744 CCAACATGAAGACGCTCCTC 58.636 55.000 0.00 0.00 0.00 3.71
2970 6219 5.065218 CCTCTGTTTATATTCGCTGCTTTGT 59.935 40.000 0.00 0.00 0.00 2.83
3017 6266 8.889849 AGTAAATCAAACACGTATTGCATTAC 57.110 30.769 19.47 19.47 33.52 1.89
3083 6334 3.999229 CACTTGTCTCGGTGCTATTTC 57.001 47.619 0.00 0.00 0.00 2.17
3093 6344 2.802816 CGGTGCTATTTCTGATACTGCC 59.197 50.000 0.00 0.00 0.00 4.85
3103 6354 2.516930 ATACTGCCATGGTGCCGC 60.517 61.111 14.67 0.00 0.00 6.53
3166 6417 6.749118 CAGTCCATCTGCAGTTTAAAATTAGC 59.251 38.462 14.67 0.00 37.36 3.09
3220 6471 4.246458 ACTTTTGGTTTAAAACGCAGCAA 58.754 34.783 0.00 0.00 34.66 3.91
3270 6521 3.196469 TGGCTGATGTTAAGTCAGGAGAG 59.804 47.826 15.78 0.00 42.58 3.20
3310 6561 4.530875 TGCACAATTTTTGGTGGGAAAAT 58.469 34.783 0.00 0.00 38.09 1.82
3339 6590 3.031736 ACCTGTGTACTTGATATCGGCT 58.968 45.455 0.00 0.00 0.00 5.52
3351 6602 0.396556 TATCGGCTGTAGTCCTGGCA 60.397 55.000 0.00 0.00 37.41 4.92
3363 6614 3.285484 AGTCCTGGCAATGATGAACATC 58.715 45.455 7.73 7.73 38.38 3.06
3428 6679 3.249189 GTGCAGGGGAGGGTGACA 61.249 66.667 0.00 0.00 0.00 3.58
3500 6751 2.124151 GGAAGGGTCATGCCGCAT 60.124 61.111 0.00 0.00 38.44 4.73
3546 6797 2.002018 TTCCCCGGTTGCTTTGTCCT 62.002 55.000 0.00 0.00 0.00 3.85
3663 6916 4.826274 AGGCACAGCAATAGAGAGTTTA 57.174 40.909 0.00 0.00 0.00 2.01
3696 6949 2.618053 CTTTACCGGCTGTAGGAACTG 58.382 52.381 0.00 0.00 41.52 3.16
3697 6950 0.899720 TTACCGGCTGTAGGAACTGG 59.100 55.000 0.00 0.00 41.52 4.00
3702 6975 0.909623 GGCTGTAGGAACTGGGCTTA 59.090 55.000 0.00 0.00 41.52 3.09
3746 7019 1.251251 AGCTGTTGCCACTGAATTCC 58.749 50.000 2.27 0.00 40.80 3.01
3832 7106 4.060205 TGATGTATCATGCGTGGAATGAG 58.940 43.478 5.98 0.00 37.46 2.90
3844 7118 4.676196 GCGTGGAATGAGCATTTTGAATCT 60.676 41.667 0.00 0.00 0.00 2.40
3895 7169 4.848841 CGTGCTATTATTTCGTTGTTTGCA 59.151 37.500 0.00 0.00 0.00 4.08
3931 7205 8.887036 AGTTTGATATATTCTAACATGTCGCA 57.113 30.769 0.00 0.00 40.98 5.10
3933 7207 8.978539 GTTTGATATATTCTAACATGTCGCAGA 58.021 33.333 0.00 0.00 39.14 4.26
3934 7208 9.710900 TTTGATATATTCTAACATGTCGCAGAT 57.289 29.630 0.00 0.00 40.67 2.90
3985 7264 2.622942 TGAAGGCAGCACGAAAAGAAAT 59.377 40.909 0.00 0.00 0.00 2.17
4013 7292 7.208777 TGATCAGCTGAATCTTATGAACTCTC 58.791 38.462 22.50 8.81 0.00 3.20
4026 7680 1.536073 AACTCTCGCACCAGCTGCTA 61.536 55.000 8.66 0.00 44.64 3.49
4036 7690 0.034186 CCAGCTGCTACCCCAATGAA 60.034 55.000 8.66 0.00 0.00 2.57
4070 7724 8.103305 AGAGAAACCAAGATGTAGAAGCAAATA 58.897 33.333 0.00 0.00 0.00 1.40
4078 7733 4.844349 TGTAGAAGCAAATAGAAGCCCT 57.156 40.909 0.00 0.00 0.00 5.19
4087 7742 4.641989 GCAAATAGAAGCCCTCTGATGAAA 59.358 41.667 0.00 0.00 35.41 2.69
4094 7749 2.887152 AGCCCTCTGATGAAACAAACAC 59.113 45.455 0.00 0.00 0.00 3.32
4098 7753 3.254166 CCTCTGATGAAACAAACACCAGG 59.746 47.826 0.00 0.00 0.00 4.45
4100 7755 4.531854 TCTGATGAAACAAACACCAGGAA 58.468 39.130 0.00 0.00 0.00 3.36
4113 7768 0.527565 CCAGGAACAAATGGAAGCCG 59.472 55.000 0.00 0.00 39.02 5.52
4147 7802 5.104527 CCATACACCAGTAGGAAATGGAAGA 60.105 44.000 0.00 0.00 40.87 2.87
4156 7811 3.747852 AGGAAATGGAAGACCCCAGATA 58.252 45.455 0.00 0.00 39.97 1.98
4245 7900 3.984838 TGGAACAAATGCCAGCAAC 57.015 47.368 0.00 0.00 31.92 4.17
4246 7901 1.117994 TGGAACAAATGCCAGCAACA 58.882 45.000 0.00 0.00 31.92 3.33
4251 7906 4.319694 GGAACAAATGCCAGCAACAAAATC 60.320 41.667 0.00 0.00 0.00 2.17
4265 7920 9.767684 CAGCAACAAAATCGTAATATTCTAACA 57.232 29.630 0.00 0.00 0.00 2.41
4316 7971 6.276847 AGCTAAGCACACAGAGATGTTATAC 58.723 40.000 0.00 0.00 0.00 1.47
4318 7973 6.199908 GCTAAGCACACAGAGATGTTATACAG 59.800 42.308 0.00 0.00 0.00 2.74
4358 8013 5.128205 CAGAATCTCATGGTGCCAGATTTA 58.872 41.667 7.73 0.00 30.44 1.40
4400 8055 3.218453 CGATGTCAGACTGGATCTAGGT 58.782 50.000 11.17 0.00 35.15 3.08
4401 8056 3.004210 CGATGTCAGACTGGATCTAGGTG 59.996 52.174 11.17 7.60 35.15 4.00
4402 8057 2.103373 TGTCAGACTGGATCTAGGTGC 58.897 52.381 11.17 5.05 35.15 5.01
4418 8073 3.679389 AGGTGCTGTTGAACATAGAAGG 58.321 45.455 0.00 0.00 0.00 3.46
4424 8079 4.019174 CTGTTGAACATAGAAGGGGCATT 58.981 43.478 0.00 0.00 0.00 3.56
4428 8083 5.387113 TGAACATAGAAGGGGCATTACAT 57.613 39.130 0.00 0.00 0.00 2.29
4434 8089 4.046286 AGAAGGGGCATTACATCACAAA 57.954 40.909 0.00 0.00 0.00 2.83
4440 8095 8.725606 AAGGGGCATTACATCACAAAATATAT 57.274 30.769 0.00 0.00 0.00 0.86
4441 8096 9.821240 AAGGGGCATTACATCACAAAATATATA 57.179 29.630 0.00 0.00 0.00 0.86
4467 8122 5.748402 TGTAATCTGGAGCATTGAAGTGAT 58.252 37.500 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.594725 TGCACAAAATAAAGAAGGTGGTACA 59.405 36.000 0.00 0.00 0.00 2.90
10 11 6.079424 TGCACAAAATAAAGAAGGTGGTAC 57.921 37.500 0.00 0.00 0.00 3.34
11 12 6.491745 TGATGCACAAAATAAAGAAGGTGGTA 59.508 34.615 0.00 0.00 0.00 3.25
12 13 5.304101 TGATGCACAAAATAAAGAAGGTGGT 59.696 36.000 0.00 0.00 0.00 4.16
13 14 5.782047 TGATGCACAAAATAAAGAAGGTGG 58.218 37.500 0.00 0.00 0.00 4.61
14 15 5.865552 CCTGATGCACAAAATAAAGAAGGTG 59.134 40.000 0.00 0.00 0.00 4.00
15 16 5.539955 ACCTGATGCACAAAATAAAGAAGGT 59.460 36.000 0.00 0.00 0.00 3.50
16 17 5.865552 CACCTGATGCACAAAATAAAGAAGG 59.134 40.000 0.00 0.00 0.00 3.46
17 18 6.449698 ACACCTGATGCACAAAATAAAGAAG 58.550 36.000 0.00 0.00 0.00 2.85
18 19 6.403866 ACACCTGATGCACAAAATAAAGAA 57.596 33.333 0.00 0.00 0.00 2.52
19 20 7.701539 ATACACCTGATGCACAAAATAAAGA 57.298 32.000 0.00 0.00 0.00 2.52
20 21 8.131100 CCTATACACCTGATGCACAAAATAAAG 58.869 37.037 0.00 0.00 0.00 1.85
21 22 7.068103 CCCTATACACCTGATGCACAAAATAAA 59.932 37.037 0.00 0.00 0.00 1.40
22 23 6.545666 CCCTATACACCTGATGCACAAAATAA 59.454 38.462 0.00 0.00 0.00 1.40
23 24 6.061441 CCCTATACACCTGATGCACAAAATA 58.939 40.000 0.00 0.00 0.00 1.40
24 25 4.889409 CCCTATACACCTGATGCACAAAAT 59.111 41.667 0.00 0.00 0.00 1.82
25 26 4.263727 ACCCTATACACCTGATGCACAAAA 60.264 41.667 0.00 0.00 0.00 2.44
26 27 3.265737 ACCCTATACACCTGATGCACAAA 59.734 43.478 0.00 0.00 0.00 2.83
27 28 2.843730 ACCCTATACACCTGATGCACAA 59.156 45.455 0.00 0.00 0.00 3.33
28 29 2.434336 GACCCTATACACCTGATGCACA 59.566 50.000 0.00 0.00 0.00 4.57
29 30 2.545952 CGACCCTATACACCTGATGCAC 60.546 54.545 0.00 0.00 0.00 4.57
30 31 1.686587 CGACCCTATACACCTGATGCA 59.313 52.381 0.00 0.00 0.00 3.96
31 32 1.961394 TCGACCCTATACACCTGATGC 59.039 52.381 0.00 0.00 0.00 3.91
32 33 4.873746 ATTCGACCCTATACACCTGATG 57.126 45.455 0.00 0.00 0.00 3.07
33 34 8.660295 TTATAATTCGACCCTATACACCTGAT 57.340 34.615 0.00 0.00 0.00 2.90
34 35 8.481492 TTTATAATTCGACCCTATACACCTGA 57.519 34.615 0.00 0.00 0.00 3.86
35 36 9.550406 TTTTTATAATTCGACCCTATACACCTG 57.450 33.333 0.00 0.00 0.00 4.00
60 61 6.468956 CGCTTGCAATGTACTTCGATATTTTT 59.531 34.615 0.00 0.00 0.00 1.94
61 62 5.965334 CGCTTGCAATGTACTTCGATATTTT 59.035 36.000 0.00 0.00 0.00 1.82
62 63 5.293324 TCGCTTGCAATGTACTTCGATATTT 59.707 36.000 0.00 0.00 0.00 1.40
63 64 4.808895 TCGCTTGCAATGTACTTCGATATT 59.191 37.500 0.00 0.00 0.00 1.28
64 65 4.368315 TCGCTTGCAATGTACTTCGATAT 58.632 39.130 0.00 0.00 0.00 1.63
65 66 3.776340 TCGCTTGCAATGTACTTCGATA 58.224 40.909 0.00 0.00 0.00 2.92
66 67 2.616960 TCGCTTGCAATGTACTTCGAT 58.383 42.857 0.00 0.00 0.00 3.59
67 68 2.073117 TCGCTTGCAATGTACTTCGA 57.927 45.000 0.00 0.00 0.00 3.71
68 69 2.873170 TTCGCTTGCAATGTACTTCG 57.127 45.000 0.00 0.00 0.00 3.79
69 70 6.106877 TCTAATTCGCTTGCAATGTACTTC 57.893 37.500 0.00 0.00 0.00 3.01
70 71 6.683974 ATCTAATTCGCTTGCAATGTACTT 57.316 33.333 0.00 0.00 0.00 2.24
71 72 6.238484 GGAATCTAATTCGCTTGCAATGTACT 60.238 38.462 0.00 0.00 40.17 2.73
72 73 5.909610 GGAATCTAATTCGCTTGCAATGTAC 59.090 40.000 0.00 0.00 40.17 2.90
73 74 5.588246 TGGAATCTAATTCGCTTGCAATGTA 59.412 36.000 0.00 0.00 40.17 2.29
74 75 4.398988 TGGAATCTAATTCGCTTGCAATGT 59.601 37.500 0.00 0.00 40.17 2.71
75 76 4.923893 TGGAATCTAATTCGCTTGCAATG 58.076 39.130 0.00 0.00 40.17 2.82
76 77 5.581126 TTGGAATCTAATTCGCTTGCAAT 57.419 34.783 0.00 0.00 40.17 3.56
77 78 5.581126 ATTGGAATCTAATTCGCTTGCAA 57.419 34.783 0.00 0.00 40.17 4.08
78 79 5.581126 AATTGGAATCTAATTCGCTTGCA 57.419 34.783 0.00 0.00 40.17 4.08
79 80 6.729187 AGTAATTGGAATCTAATTCGCTTGC 58.271 36.000 7.85 0.00 40.17 4.01
80 81 9.573133 AAAAGTAATTGGAATCTAATTCGCTTG 57.427 29.630 7.85 0.00 40.17 4.01
110 111 9.461312 ACACATAGAAAGATAGGCAATAACAAA 57.539 29.630 0.00 0.00 0.00 2.83
111 112 8.892723 CACACATAGAAAGATAGGCAATAACAA 58.107 33.333 0.00 0.00 0.00 2.83
112 113 8.046708 ACACACATAGAAAGATAGGCAATAACA 58.953 33.333 0.00 0.00 0.00 2.41
113 114 8.438676 ACACACATAGAAAGATAGGCAATAAC 57.561 34.615 0.00 0.00 0.00 1.89
116 117 9.461312 TTTTACACACATAGAAAGATAGGCAAT 57.539 29.630 0.00 0.00 0.00 3.56
117 118 8.856153 TTTTACACACATAGAAAGATAGGCAA 57.144 30.769 0.00 0.00 0.00 4.52
118 119 9.461312 AATTTTACACACATAGAAAGATAGGCA 57.539 29.630 0.00 0.00 0.00 4.75
149 150 9.182933 GCATTTGAAAATTTGTATTTGTTGCAT 57.817 25.926 0.00 0.00 34.27 3.96
150 151 7.646922 GGCATTTGAAAATTTGTATTTGTTGCA 59.353 29.630 0.00 0.00 34.27 4.08
151 152 7.114670 GGGCATTTGAAAATTTGTATTTGTTGC 59.885 33.333 0.00 0.00 34.27 4.17
152 153 7.323177 CGGGCATTTGAAAATTTGTATTTGTTG 59.677 33.333 0.00 0.00 34.27 3.33
153 154 7.012799 ACGGGCATTTGAAAATTTGTATTTGTT 59.987 29.630 0.00 0.00 34.27 2.83
154 155 6.484977 ACGGGCATTTGAAAATTTGTATTTGT 59.515 30.769 0.00 0.00 34.27 2.83
155 156 6.796072 CACGGGCATTTGAAAATTTGTATTTG 59.204 34.615 0.00 0.00 34.27 2.32
156 157 6.072783 CCACGGGCATTTGAAAATTTGTATTT 60.073 34.615 0.00 0.00 35.49 1.40
157 158 5.411053 CCACGGGCATTTGAAAATTTGTATT 59.589 36.000 0.00 0.00 0.00 1.89
158 159 4.934602 CCACGGGCATTTGAAAATTTGTAT 59.065 37.500 0.00 0.00 0.00 2.29
159 160 4.310769 CCACGGGCATTTGAAAATTTGTA 58.689 39.130 0.00 0.00 0.00 2.41
160 161 3.137533 CCACGGGCATTTGAAAATTTGT 58.862 40.909 0.00 0.00 0.00 2.83
161 162 3.809918 CCACGGGCATTTGAAAATTTG 57.190 42.857 0.00 0.00 0.00 2.32
178 179 1.772063 GACTGTCCGTGTGTTGCCAC 61.772 60.000 0.00 0.00 42.19 5.01
179 180 1.522806 GACTGTCCGTGTGTTGCCA 60.523 57.895 0.00 0.00 0.00 4.92
180 181 0.032952 TAGACTGTCCGTGTGTTGCC 59.967 55.000 3.76 0.00 0.00 4.52
181 182 1.137513 GTAGACTGTCCGTGTGTTGC 58.862 55.000 3.76 0.00 0.00 4.17
182 183 2.795175 AGTAGACTGTCCGTGTGTTG 57.205 50.000 3.76 0.00 0.00 3.33
183 184 3.484407 ACTAGTAGACTGTCCGTGTGTT 58.516 45.455 3.59 0.00 0.00 3.32
184 185 3.137446 ACTAGTAGACTGTCCGTGTGT 57.863 47.619 3.59 0.00 0.00 3.72
185 186 5.618056 TTTACTAGTAGACTGTCCGTGTG 57.382 43.478 3.59 0.00 0.00 3.82
186 187 7.555554 ACATATTTACTAGTAGACTGTCCGTGT 59.444 37.037 3.59 0.14 0.00 4.49
187 188 7.928103 ACATATTTACTAGTAGACTGTCCGTG 58.072 38.462 3.59 0.00 0.00 4.94
188 189 9.618890 TTACATATTTACTAGTAGACTGTCCGT 57.381 33.333 3.59 0.00 0.00 4.69
367 372 2.823196 TCTTGCAACTGTTTCGTGTG 57.177 45.000 0.00 0.00 0.00 3.82
371 376 2.535574 GCCTTTTCTTGCAACTGTTTCG 59.464 45.455 0.00 0.00 0.00 3.46
382 387 8.592155 GCTTTATTTATTTACCGCCTTTTCTTG 58.408 33.333 0.00 0.00 0.00 3.02
385 390 6.197655 CCGCTTTATTTATTTACCGCCTTTTC 59.802 38.462 0.00 0.00 0.00 2.29
388 394 4.037089 CCCGCTTTATTTATTTACCGCCTT 59.963 41.667 0.00 0.00 0.00 4.35
432 438 2.093394 CCAAAAACCCCTCCGTTGTTTT 60.093 45.455 0.00 0.00 42.30 2.43
434 440 1.116308 CCAAAAACCCCTCCGTTGTT 58.884 50.000 0.00 0.00 0.00 2.83
436 442 1.272212 CATCCAAAAACCCCTCCGTTG 59.728 52.381 0.00 0.00 0.00 4.10
437 443 1.133294 ACATCCAAAAACCCCTCCGTT 60.133 47.619 0.00 0.00 0.00 4.44
439 445 0.887933 CACATCCAAAAACCCCTCCG 59.112 55.000 0.00 0.00 0.00 4.63
440 446 1.203125 TCCACATCCAAAAACCCCTCC 60.203 52.381 0.00 0.00 0.00 4.30
564 581 1.560505 AAATTTGAAGCGGGCCTCAT 58.439 45.000 0.84 0.00 0.00 2.90
570 587 7.600752 TCCAAATAAGTTAAAATTTGAAGCGGG 59.399 33.333 15.57 4.11 42.90 6.13
584 601 7.496346 ACTCCTCAGATGTCCAAATAAGTTA 57.504 36.000 0.00 0.00 0.00 2.24
587 604 6.648192 AGAACTCCTCAGATGTCCAAATAAG 58.352 40.000 0.00 0.00 0.00 1.73
589 606 5.163509 CGAGAACTCCTCAGATGTCCAAATA 60.164 44.000 0.00 0.00 42.06 1.40
595 612 1.202359 GCCGAGAACTCCTCAGATGTC 60.202 57.143 0.00 0.00 42.06 3.06
644 662 4.893424 ACAGTGCGTGAACAGTATTTTT 57.107 36.364 0.00 0.00 0.00 1.94
646 664 4.024893 CAGAACAGTGCGTGAACAGTATTT 60.025 41.667 0.00 0.00 0.00 1.40
647 665 3.494626 CAGAACAGTGCGTGAACAGTATT 59.505 43.478 0.00 0.00 0.00 1.89
648 666 3.059884 CAGAACAGTGCGTGAACAGTAT 58.940 45.455 0.00 0.00 0.00 2.12
691 709 5.583854 TCATTTAGACATTTGAGCAGCTCTC 59.416 40.000 23.15 11.79 42.23 3.20
709 727 6.811170 GGTCCGCTTCAATTTCAATTCATTTA 59.189 34.615 0.00 0.00 0.00 1.40
725 743 1.733399 GACGTGTGAGGTCCGCTTC 60.733 63.158 0.00 0.00 0.00 3.86
800 855 5.047731 CAGGCTCATCTATTCCAGATACGAA 60.048 44.000 0.00 0.00 42.40 3.85
801 856 4.460731 CAGGCTCATCTATTCCAGATACGA 59.539 45.833 0.00 0.00 42.40 3.43
802 857 4.381398 CCAGGCTCATCTATTCCAGATACG 60.381 50.000 0.00 0.00 42.40 3.06
804 859 4.099633 CCCAGGCTCATCTATTCCAGATA 58.900 47.826 0.00 0.00 42.40 1.98
805 860 2.911636 CCCAGGCTCATCTATTCCAGAT 59.088 50.000 0.00 0.00 45.35 2.90
806 861 2.333069 CCCAGGCTCATCTATTCCAGA 58.667 52.381 0.00 0.00 37.79 3.86
807 862 1.271271 GCCCAGGCTCATCTATTCCAG 60.271 57.143 0.08 0.00 38.26 3.86
808 863 0.767375 GCCCAGGCTCATCTATTCCA 59.233 55.000 0.08 0.00 38.26 3.53
809 864 0.767375 TGCCCAGGCTCATCTATTCC 59.233 55.000 10.58 0.00 42.51 3.01
811 866 0.475906 GGTGCCCAGGCTCATCTATT 59.524 55.000 10.58 0.00 42.51 1.73
812 867 1.762522 CGGTGCCCAGGCTCATCTAT 61.763 60.000 10.58 0.00 42.51 1.98
813 868 2.434843 CGGTGCCCAGGCTCATCTA 61.435 63.158 10.58 0.00 42.51 1.98
986 1073 3.133014 CCATGTCCGGAGCTCGAT 58.867 61.111 3.06 0.00 42.43 3.59
987 1074 3.838271 GCCATGTCCGGAGCTCGA 61.838 66.667 3.06 0.00 42.43 4.04
1159 1246 1.829096 GTAGGCGGAGAGGGGAGAC 60.829 68.421 0.00 0.00 0.00 3.36
1175 1262 3.232483 TTGTGTCCGTGGCCCGTA 61.232 61.111 0.00 0.00 33.66 4.02
1195 1282 2.990066 AATCGAAGAAGAATCCGGCT 57.010 45.000 0.00 0.00 43.58 5.52
1207 1294 2.279136 CAGCGACGGTAAGAAATCGAAG 59.721 50.000 0.00 0.00 36.70 3.79
1231 1318 0.389391 CGTATTCACCTGGCGGAGAT 59.611 55.000 0.00 0.00 29.70 2.75
1356 1443 3.435186 GAACGCCCTGGAAGCAGC 61.435 66.667 0.00 0.00 0.00 5.25
1374 1461 1.355381 TGACCCACTGGAAGCATCATT 59.645 47.619 0.00 0.00 37.60 2.57
1375 1462 0.994247 TGACCCACTGGAAGCATCAT 59.006 50.000 0.00 0.00 37.60 2.45
1463 1593 2.286523 CGCCTTCCTCTGGTGGTCT 61.287 63.158 0.00 0.00 0.00 3.85
1533 1663 1.813786 CGGTATCTTCCGGATCTCCTC 59.186 57.143 4.15 0.00 45.88 3.71
1597 1727 0.825840 GCCATAGGCTCTCGAGTCCT 60.826 60.000 24.58 24.58 46.69 3.85
1613 1743 3.197766 CAGTAGAATGTCTTACTGGGCCA 59.802 47.826 5.85 5.85 37.02 5.36
1619 1749 4.615513 AGGGAGCAGTAGAATGTCTTACT 58.384 43.478 0.00 0.00 0.00 2.24
1659 1793 3.056536 ACAGATCTTTCTAGCAAGACGCA 60.057 43.478 6.99 0.00 46.13 5.24
1661 1795 6.302615 CAAAACAGATCTTTCTAGCAAGACG 58.697 40.000 6.99 2.33 35.57 4.18
1675 1812 9.428097 AGGATTAAAATCTTTGCAAAACAGATC 57.572 29.630 13.84 9.78 35.73 2.75
1680 1817 7.961325 TCCAGGATTAAAATCTTTGCAAAAC 57.039 32.000 13.84 0.00 35.73 2.43
1697 1834 2.357154 CGTTCCAGGGAAATTCCAGGAT 60.357 50.000 21.01 0.33 40.45 3.24
1739 1876 3.670625 CAGGGGTGACTAAATCGTTGAA 58.329 45.455 0.00 0.00 0.00 2.69
1774 1911 3.577649 TTTCGAGAGACTCTTCGCAAT 57.422 42.857 6.40 0.00 41.84 3.56
1807 1945 4.530553 TCTCAGTACAAATTCAGTGGCCTA 59.469 41.667 3.32 0.00 0.00 3.93
1824 1962 6.183361 ACCCTATTTGAAACAAGTCTCTCAGT 60.183 38.462 0.00 0.00 0.00 3.41
1833 1971 7.362920 CCTGATGGTAACCCTATTTGAAACAAG 60.363 40.741 0.00 0.00 0.00 3.16
1848 1986 2.493547 GGCTTGGCCTGATGGTAAC 58.506 57.895 3.32 0.00 46.69 2.50
1895 2033 5.598417 ACATTTGCTCCTTTGGTTAGTTCTT 59.402 36.000 0.00 0.00 0.00 2.52
1970 2372 8.735692 TGATATTCACTTTGATATGCAAGTCA 57.264 30.769 0.00 0.00 37.87 3.41
1976 2378 8.613060 TCCTCTTGATATTCACTTTGATATGC 57.387 34.615 0.00 0.00 0.00 3.14
2019 2421 3.657398 TGGCCAGTGATGATGAGAATT 57.343 42.857 0.00 0.00 0.00 2.17
2051 2453 1.390565 GAGAGCAGCTCATTGGCAAT 58.609 50.000 24.64 6.96 43.38 3.56
2063 2465 0.612229 TGGAGAAAGCAGGAGAGCAG 59.388 55.000 0.00 0.00 36.85 4.24
2067 2469 0.541998 TCGGTGGAGAAAGCAGGAGA 60.542 55.000 0.00 0.00 0.00 3.71
2069 2471 1.544825 CCTCGGTGGAGAAAGCAGGA 61.545 60.000 0.00 0.00 43.27 3.86
2087 2489 2.302587 TGGGGTTTTCCAGATGAACC 57.697 50.000 0.00 0.00 42.91 3.62
2115 2517 3.462483 TCTAGCAAAGTTTGACCGTGA 57.538 42.857 19.82 6.48 0.00 4.35
2155 2557 3.936372 TCCTTGGACTCTTTCTACACG 57.064 47.619 0.00 0.00 0.00 4.49
2177 2579 4.403453 GTCAATTATCTTTGCACGTGTCC 58.597 43.478 18.38 1.32 0.00 4.02
2254 2656 6.509677 CGTTGGACTCTTTTCTCACTTTACAC 60.510 42.308 0.00 0.00 0.00 2.90
2388 2791 5.010314 ACTCACGGACACTTGTCTAAACATA 59.990 40.000 9.20 0.00 44.20 2.29
2390 2793 3.131577 ACTCACGGACACTTGTCTAAACA 59.868 43.478 9.20 0.00 44.20 2.83
2598 4524 4.002982 TGTCATGGCACTAACTTGATGTC 58.997 43.478 0.00 0.00 0.00 3.06
2678 4604 8.948631 TCTCATGTATCAGAAAATACAAGGAC 57.051 34.615 1.27 0.00 43.40 3.85
2680 4606 9.994432 GTTTCTCATGTATCAGAAAATACAAGG 57.006 33.333 8.44 0.00 43.40 3.61
2773 6022 6.896021 TCTTAACTGGGATCTCTAATACCG 57.104 41.667 0.00 0.00 0.00 4.02
2780 6029 9.621239 TCCAATTATATCTTAACTGGGATCTCT 57.379 33.333 0.00 0.00 0.00 3.10
2886 6135 2.689553 TGTTGGCTCGATTCTATGCA 57.310 45.000 0.00 0.00 0.00 3.96
2891 6140 3.265791 GTCTTCATGTTGGCTCGATTCT 58.734 45.455 0.00 0.00 0.00 2.40
2911 6160 1.304052 ACTCAGAGCAGAGGAGCGT 60.304 57.895 0.00 0.00 39.97 5.07
2919 6168 3.523606 AGATAGCAACACTCAGAGCAG 57.476 47.619 0.00 0.00 0.00 4.24
2959 6208 2.224185 TGGAACTAGAACAAAGCAGCGA 60.224 45.455 0.00 0.00 0.00 4.93
2960 6209 2.143122 TGGAACTAGAACAAAGCAGCG 58.857 47.619 0.00 0.00 0.00 5.18
2970 6219 7.241042 ACTACAATACAAGCTGGAACTAGAA 57.759 36.000 0.00 0.00 0.00 2.10
3017 6266 7.282585 TGGATTAGACAGTTATTCCATTGAGG 58.717 38.462 0.00 0.00 31.50 3.86
3031 6280 4.619973 CTCTGCTAAGCTGGATTAGACAG 58.380 47.826 9.42 13.57 37.76 3.51
3055 6306 1.597854 CGAGACAAGTGCAAGCCCA 60.598 57.895 0.00 0.00 0.00 5.36
3083 6334 1.162181 CGGCACCATGGCAGTATCAG 61.162 60.000 13.04 0.00 43.94 2.90
3093 6344 2.211619 AAATTGGACGCGGCACCATG 62.212 55.000 17.00 0.00 36.02 3.66
3103 6354 3.058501 GGTGACAGTAACCAAATTGGACG 60.059 47.826 20.25 6.59 40.96 4.79
3158 6409 8.230472 CAGTATTCTGGATTCAGGCTAATTTT 57.770 34.615 0.00 0.00 41.23 1.82
3193 6444 6.859508 GCTGCGTTTTAAACCAAAAGTACTAT 59.140 34.615 0.00 0.00 36.79 2.12
3199 6450 4.092091 TGTTGCTGCGTTTTAAACCAAAAG 59.908 37.500 1.97 0.00 36.79 2.27
3238 6489 6.677913 ACTTAACATCAGCCACAAATGTAAC 58.322 36.000 0.00 0.00 33.42 2.50
3276 6527 7.151308 CCAAAAATTGTGCAACCTAAGACATA 58.849 34.615 0.00 0.00 34.36 2.29
3284 6535 2.421248 CCCACCAAAAATTGTGCAACCT 60.421 45.455 0.00 0.00 34.36 3.50
3295 6546 4.651503 TGTGCTCTATTTTCCCACCAAAAA 59.348 37.500 0.00 0.00 0.00 1.94
3327 6578 3.305676 CCAGGACTACAGCCGATATCAAG 60.306 52.174 3.12 0.00 0.00 3.02
3333 6584 1.264749 TTGCCAGGACTACAGCCGAT 61.265 55.000 0.00 0.00 0.00 4.18
3336 6587 0.253044 TCATTGCCAGGACTACAGCC 59.747 55.000 0.00 0.00 0.00 4.85
3339 6590 3.008923 TGTTCATCATTGCCAGGACTACA 59.991 43.478 0.00 0.00 0.00 2.74
3363 6614 7.274250 GCAGCAGACAACAAAAGGATAATAAAG 59.726 37.037 0.00 0.00 0.00 1.85
3402 6653 1.852157 TCCCCTGCACCAGACCAAT 60.852 57.895 0.00 0.00 32.44 3.16
3500 6751 0.178958 GGGGAGGCTAGAGATTCCGA 60.179 60.000 0.00 0.00 0.00 4.55
3546 6797 4.484236 CTGTGAGAACAAACAAAACTGCA 58.516 39.130 0.00 0.00 0.00 4.41
3663 6916 4.019591 AGCCGGTAAAGGTTACAGAAGAAT 60.020 41.667 1.90 0.00 0.00 2.40
3702 6975 3.155897 CCTAGCAGGCTCCTACCAT 57.844 57.895 0.00 0.00 0.00 3.55
3746 7019 0.321671 AACACACCGGATCCACAGAG 59.678 55.000 9.46 0.94 0.00 3.35
3832 7106 4.355543 TCGGCTTGTAGATTCAAAATGC 57.644 40.909 0.00 0.00 0.00 3.56
3937 7211 9.713740 GCAAGTACTTTGAGATCATTTATCTTG 57.286 33.333 5.07 0.00 45.35 3.02
3985 7264 6.099413 AGTTCATAAGATTCAGCTGATCAGGA 59.901 38.462 23.89 10.96 0.00 3.86
4026 7680 1.780309 TCTGTGGTCTTTCATTGGGGT 59.220 47.619 0.00 0.00 0.00 4.95
4036 7690 4.141390 ACATCTTGGTTTCTCTGTGGTCTT 60.141 41.667 0.00 0.00 0.00 3.01
4070 7724 3.795688 TTGTTTCATCAGAGGGCTTCT 57.204 42.857 0.00 0.00 36.25 2.85
4078 7733 4.163441 TCCTGGTGTTTGTTTCATCAGA 57.837 40.909 7.62 0.00 44.08 3.27
4087 7742 3.370104 TCCATTTGTTCCTGGTGTTTGT 58.630 40.909 0.00 0.00 34.03 2.83
4094 7749 0.527565 CGGCTTCCATTTGTTCCTGG 59.472 55.000 0.00 0.00 0.00 4.45
4098 7753 1.202114 TCATGCGGCTTCCATTTGTTC 59.798 47.619 0.00 0.00 0.00 3.18
4100 7755 1.406539 GATCATGCGGCTTCCATTTGT 59.593 47.619 0.00 0.00 0.00 2.83
4113 7768 2.224606 CTGGTGTATGGGTGATCATGC 58.775 52.381 0.00 0.00 0.00 4.06
4147 7802 4.202673 ACTGGTGTTTGATTTATCTGGGGT 60.203 41.667 0.00 0.00 0.00 4.95
4156 7811 6.068010 TCCATCTGTTACTGGTGTTTGATTT 58.932 36.000 2.05 0.00 34.03 2.17
4188 7843 1.452145 CCCTGGTGTTTGGTCCAACG 61.452 60.000 2.98 0.00 33.06 4.10
4347 8002 6.374333 TCAGGTTAAGTTGATAAATCTGGCAC 59.626 38.462 0.00 0.00 0.00 5.01
4358 8013 3.865745 CGCGAGATTCAGGTTAAGTTGAT 59.134 43.478 0.00 0.00 0.00 2.57
4400 8055 2.879756 GCCCCTTCTATGTTCAACAGCA 60.880 50.000 0.00 0.00 0.00 4.41
4401 8056 1.745653 GCCCCTTCTATGTTCAACAGC 59.254 52.381 0.00 0.00 0.00 4.40
4402 8057 3.071874 TGCCCCTTCTATGTTCAACAG 57.928 47.619 0.00 0.00 0.00 3.16
4418 8073 9.243105 AGGTATATATTTTGTGATGTAATGCCC 57.757 33.333 0.00 0.00 0.00 5.36
4434 8089 9.896645 CAATGCTCCAGATTACAGGTATATATT 57.103 33.333 0.00 0.00 0.00 1.28
4440 8095 5.189736 ACTTCAATGCTCCAGATTACAGGTA 59.810 40.000 0.00 0.00 0.00 3.08
4441 8096 4.018960 ACTTCAATGCTCCAGATTACAGGT 60.019 41.667 0.00 0.00 0.00 4.00
4467 8122 6.907853 TTGACACATCCATGGTGAAAATTA 57.092 33.333 12.58 0.00 39.53 1.40



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

AutoCloner maintained by Alex Coulton.