Multiple sequence alignment - TraesCS3D01G129800

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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 TraesCS3D01G129800 chr3D 100.000 2101 0 0 945 3045 89896229 89898329 0.000000e+00 3880.0
1 TraesCS3D01G129800 chr3D 100.000 642 0 0 1 642 89895285 89895926 0.000000e+00 1186.0
2 TraesCS3D01G129800 chr3D 93.043 115 6 2 1 115 579700281 579700169 1.880000e-37 167.0
3 TraesCS3D01G129800 chr3D 96.842 95 3 0 4 98 481537599 481537505 3.140000e-35 159.0
4 TraesCS3D01G129800 chr3D 90.164 61 5 1 491 551 89895732 89895791 9.050000e-11 78.7
5 TraesCS3D01G129800 chr3D 90.164 61 5 1 448 507 89895775 89895835 9.050000e-11 78.7
6 TraesCS3D01G129800 chr3B 89.897 2138 126 55 951 3042 139407518 139409611 0.000000e+00 2669.0
7 TraesCS3D01G129800 chr3B 83.120 391 22 26 129 507 139406969 139407327 1.760000e-82 316.0
8 TraesCS3D01G129800 chr3B 97.101 138 4 0 501 638 139407277 139407414 1.830000e-57 233.0
9 TraesCS3D01G129800 chr3A 86.010 2173 148 70 957 3045 106433038 106435138 0.000000e+00 2185.0
10 TraesCS3D01G129800 chr3A 98.851 87 1 0 542 628 106432585 106432671 4.060000e-34 156.0
11 TraesCS3D01G129800 chr3A 74.619 394 39 25 172 553 106432310 106432654 1.920000e-22 117.0
12 TraesCS3D01G129800 chr4D 97.959 98 2 0 1 98 484450611 484450514 1.450000e-38 171.0
13 TraesCS3D01G129800 chr4D 96.939 98 3 0 1 98 97721594 97721497 6.750000e-37 165.0
14 TraesCS3D01G129800 chr4D 94.898 98 5 0 1 98 43451450 43451547 1.460000e-33 154.0
15 TraesCS3D01G129800 chr2D 94.643 112 3 3 1 110 413267529 413267419 1.450000e-38 171.0
16 TraesCS3D01G129800 chr2D 96.939 98 3 0 1 98 589179958 589180055 6.750000e-37 165.0
17 TraesCS3D01G129800 chr5D 95.098 102 4 1 1 101 84191643 84191542 3.140000e-35 159.0
18 TraesCS3D01G129800 chr6D 94.898 98 5 0 1 98 160222535 160222632 1.460000e-33 154.0


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 TraesCS3D01G129800 chr3D 89895285 89898329 3044 False 1305.850000 3880 95.082000 1 3045 4 chr3D.!!$F1 3044
1 TraesCS3D01G129800 chr3B 139406969 139409611 2642 False 1072.666667 2669 90.039333 129 3042 3 chr3B.!!$F1 2913
2 TraesCS3D01G129800 chr3A 106432310 106435138 2828 False 819.333333 2185 86.493333 172 3045 3 chr3A.!!$F1 2873

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
70 71 0.035317 AGCTGCTCGATGTGTCCAAA 59.965 50.0 0.0 0.0 0.00 3.28 F
268 274 0.107066 ATCATCATTCCTGCCGTGCA 60.107 50.0 0.0 0.0 36.92 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1923 0.578683 CAGTATCTGCACCGCAATCG 59.421 55.0 0.00 0.00 38.41 3.34 R
2266 2381 0.175760 TCTTTTCCTCGGCGATCAGG 59.824 55.0 11.27 8.95 0.00 3.86 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
19 20 1.941325 GGGAACTTGTCAGATAGCGG 58.059 55.000 0.00 0.00 0.00 5.52
20 21 1.207329 GGGAACTTGTCAGATAGCGGT 59.793 52.381 0.00 0.00 0.00 5.68
21 22 2.354805 GGGAACTTGTCAGATAGCGGTT 60.355 50.000 0.00 0.00 0.00 4.44
22 23 2.673368 GGAACTTGTCAGATAGCGGTTG 59.327 50.000 0.00 0.00 0.00 3.77
23 24 3.326747 GAACTTGTCAGATAGCGGTTGT 58.673 45.455 0.00 0.00 0.00 3.32
24 25 2.688507 ACTTGTCAGATAGCGGTTGTG 58.311 47.619 0.00 0.00 0.00 3.33
25 26 2.299013 ACTTGTCAGATAGCGGTTGTGA 59.701 45.455 0.00 0.00 0.00 3.58
26 27 3.055819 ACTTGTCAGATAGCGGTTGTGAT 60.056 43.478 0.00 0.00 0.00 3.06
27 28 2.892374 TGTCAGATAGCGGTTGTGATG 58.108 47.619 0.00 0.00 0.00 3.07
28 29 2.205074 GTCAGATAGCGGTTGTGATGG 58.795 52.381 0.00 0.00 0.00 3.51
29 30 0.940126 CAGATAGCGGTTGTGATGGC 59.060 55.000 0.00 0.00 0.00 4.40
30 31 0.179045 AGATAGCGGTTGTGATGGCC 60.179 55.000 0.00 0.00 0.00 5.36
32 33 2.940890 ATAGCGGTTGTGATGGCCGG 62.941 60.000 0.00 0.00 45.02 6.13
34 35 2.124736 CGGTTGTGATGGCCGGAT 60.125 61.111 5.05 0.00 41.60 4.18
35 36 2.180204 CGGTTGTGATGGCCGGATC 61.180 63.158 5.05 0.00 41.60 3.36
36 37 2.180204 GGTTGTGATGGCCGGATCG 61.180 63.158 5.05 0.00 0.00 3.69
37 38 1.449601 GTTGTGATGGCCGGATCGT 60.450 57.895 5.05 0.00 0.00 3.73
38 39 1.449423 TTGTGATGGCCGGATCGTG 60.449 57.895 5.05 0.00 0.00 4.35
39 40 3.272334 GTGATGGCCGGATCGTGC 61.272 66.667 5.05 0.00 0.00 5.34
40 41 4.889856 TGATGGCCGGATCGTGCG 62.890 66.667 5.05 0.00 0.00 5.34
65 66 2.435586 GCCAGCTGCTCGATGTGT 60.436 61.111 8.66 0.00 36.87 3.72
66 67 2.459442 GCCAGCTGCTCGATGTGTC 61.459 63.158 8.66 0.00 36.87 3.67
67 68 1.812922 CCAGCTGCTCGATGTGTCC 60.813 63.158 8.66 0.00 0.00 4.02
68 69 1.079612 CAGCTGCTCGATGTGTCCA 60.080 57.895 0.00 0.00 0.00 4.02
69 70 0.671472 CAGCTGCTCGATGTGTCCAA 60.671 55.000 0.00 0.00 0.00 3.53
70 71 0.035317 AGCTGCTCGATGTGTCCAAA 59.965 50.000 0.00 0.00 0.00 3.28
71 72 1.089920 GCTGCTCGATGTGTCCAAAT 58.910 50.000 0.00 0.00 0.00 2.32
72 73 2.093500 AGCTGCTCGATGTGTCCAAATA 60.093 45.455 0.00 0.00 0.00 1.40
73 74 2.286294 GCTGCTCGATGTGTCCAAATAG 59.714 50.000 0.00 0.00 0.00 1.73
74 75 3.525537 CTGCTCGATGTGTCCAAATAGT 58.474 45.455 0.00 0.00 0.00 2.12
75 76 3.261580 TGCTCGATGTGTCCAAATAGTG 58.738 45.455 0.00 0.00 0.00 2.74
76 77 2.030946 GCTCGATGTGTCCAAATAGTGC 59.969 50.000 0.00 0.00 0.00 4.40
77 78 2.267426 TCGATGTGTCCAAATAGTGCG 58.733 47.619 0.00 0.00 0.00 5.34
78 79 1.999735 CGATGTGTCCAAATAGTGCGT 59.000 47.619 0.00 0.00 0.00 5.24
79 80 3.119424 TCGATGTGTCCAAATAGTGCGTA 60.119 43.478 0.00 0.00 0.00 4.42
80 81 3.802139 CGATGTGTCCAAATAGTGCGTAT 59.198 43.478 0.00 0.00 0.00 3.06
81 82 4.318050 CGATGTGTCCAAATAGTGCGTATG 60.318 45.833 0.00 0.00 0.00 2.39
82 83 2.675844 TGTGTCCAAATAGTGCGTATGC 59.324 45.455 0.00 0.00 43.20 3.14
100 101 8.614994 GCGTATGCACTTTTTAGATTTTATGT 57.385 30.769 0.89 0.00 42.15 2.29
101 102 9.710979 GCGTATGCACTTTTTAGATTTTATGTA 57.289 29.630 0.89 0.00 42.15 2.29
155 156 6.516017 GCATGCGTTTCACAAAAATGATAAAC 59.484 34.615 0.00 0.00 0.00 2.01
167 168 7.440856 ACAAAAATGATAAACATGACACCAACC 59.559 33.333 0.00 0.00 39.39 3.77
169 170 4.380843 TGATAAACATGACACCAACCCT 57.619 40.909 0.00 0.00 0.00 4.34
195 200 1.921243 TTGTCACGTCATATGCGGAG 58.079 50.000 18.99 12.94 0.00 4.63
259 265 3.532892 CGCAAGTAGCATCATCATTCC 57.467 47.619 0.00 0.00 46.13 3.01
260 266 3.136763 CGCAAGTAGCATCATCATTCCT 58.863 45.455 0.00 0.00 46.13 3.36
261 267 3.059120 CGCAAGTAGCATCATCATTCCTG 60.059 47.826 0.00 0.00 46.13 3.86
262 268 3.304525 GCAAGTAGCATCATCATTCCTGC 60.305 47.826 0.00 0.00 44.79 4.85
263 269 3.137446 AGTAGCATCATCATTCCTGCC 57.863 47.619 0.00 0.00 35.21 4.85
264 270 1.802960 GTAGCATCATCATTCCTGCCG 59.197 52.381 0.00 0.00 35.21 5.69
265 271 0.182061 AGCATCATCATTCCTGCCGT 59.818 50.000 0.00 0.00 35.21 5.68
266 272 0.309922 GCATCATCATTCCTGCCGTG 59.690 55.000 0.00 0.00 0.00 4.94
267 273 0.309922 CATCATCATTCCTGCCGTGC 59.690 55.000 0.00 0.00 0.00 5.34
268 274 0.107066 ATCATCATTCCTGCCGTGCA 60.107 50.000 0.00 0.00 36.92 4.57
269 275 0.107066 TCATCATTCCTGCCGTGCAT 60.107 50.000 0.00 0.00 38.13 3.96
270 276 0.742505 CATCATTCCTGCCGTGCATT 59.257 50.000 0.00 0.00 38.13 3.56
271 277 1.027357 ATCATTCCTGCCGTGCATTC 58.973 50.000 0.00 0.00 38.13 2.67
272 278 1.031571 TCATTCCTGCCGTGCATTCC 61.032 55.000 0.00 0.00 38.13 3.01
303 309 5.352302 GTCACGTAACGTTATGCGAATATG 58.648 41.667 24.09 14.95 44.77 1.78
307 313 3.602390 AACGTTATGCGAATATGTGCC 57.398 42.857 0.00 0.00 44.77 5.01
345 359 1.224592 CCCCTTTCGGATCCTGTGG 59.775 63.158 10.75 6.58 0.00 4.17
349 363 2.084546 CCTTTCGGATCCTGTGGAAAC 58.915 52.381 10.75 0.00 34.34 2.78
350 364 1.732259 CTTTCGGATCCTGTGGAAACG 59.268 52.381 10.75 6.87 34.34 3.60
351 365 0.672401 TTCGGATCCTGTGGAAACGC 60.672 55.000 10.75 0.00 42.66 4.84
359 373 3.595961 GTGGAAACGCAACGCAAC 58.404 55.556 0.00 0.00 41.67 4.17
360 374 2.023461 TGGAAACGCAACGCAACG 59.977 55.556 0.00 0.00 0.00 4.10
361 375 3.383601 GGAAACGCAACGCAACGC 61.384 61.111 0.00 0.00 0.00 4.84
362 376 2.649349 GAAACGCAACGCAACGCA 60.649 55.556 0.00 0.00 0.00 5.24
363 377 2.202492 AAACGCAACGCAACGCAA 60.202 50.000 0.00 0.00 0.00 4.85
364 378 1.734359 GAAACGCAACGCAACGCAAA 61.734 50.000 0.00 0.00 0.00 3.68
365 379 1.344942 AAACGCAACGCAACGCAAAA 61.345 45.000 0.00 0.00 0.00 2.44
366 380 1.738144 AACGCAACGCAACGCAAAAG 61.738 50.000 0.00 0.00 0.00 2.27
367 381 2.242386 GCAACGCAACGCAAAAGC 59.758 55.556 0.00 0.00 0.00 3.51
368 382 2.512301 GCAACGCAACGCAAAAGCA 61.512 52.632 0.00 0.00 0.00 3.91
381 395 3.424829 CGCAAAAGCAAGCTCGAGATTTA 60.425 43.478 18.75 0.00 0.00 1.40
390 404 4.895224 AGCTCGAGATTTATCACGTGTA 57.105 40.909 18.75 4.61 40.82 2.90
391 405 5.440234 AGCTCGAGATTTATCACGTGTAT 57.560 39.130 18.75 10.27 40.82 2.29
398 412 8.166066 TCGAGATTTATCACGTGTATGTTTTTG 58.834 33.333 16.51 2.76 40.82 2.44
416 432 1.604604 TGCCCCTTTTTGTCTCGAAG 58.395 50.000 0.00 0.00 0.00 3.79
417 433 1.142060 TGCCCCTTTTTGTCTCGAAGA 59.858 47.619 0.00 0.00 0.00 2.87
638 658 0.876342 GGGATCGCGTCTCATCCAAC 60.876 60.000 21.82 6.10 40.55 3.77
639 659 0.876342 GGATCGCGTCTCATCCAACC 60.876 60.000 17.15 0.00 38.84 3.77
979 1037 1.984570 TTGCTCTGTCCCTCCCTCG 60.985 63.158 0.00 0.00 0.00 4.63
992 1050 1.597302 CCCTCGCTCGTCCGATCTA 60.597 63.158 1.14 0.00 36.54 1.98
1020 1084 0.736053 CCCTTCTCTCTCCGTCTTCG 59.264 60.000 0.00 0.00 0.00 3.79
1021 1085 1.455248 CCTTCTCTCTCCGTCTTCGT 58.545 55.000 0.00 0.00 35.01 3.85
1314 1386 2.272797 CGTCTCTCCGTCTCCCCT 59.727 66.667 0.00 0.00 0.00 4.79
1316 1388 1.820481 GTCTCTCCGTCTCCCCTCG 60.820 68.421 0.00 0.00 0.00 4.63
1317 1389 2.517402 CTCTCCGTCTCCCCTCGG 60.517 72.222 0.00 0.00 46.93 4.63
1791 1877 1.281867 CCCTCCCAGCACAATTGTCTA 59.718 52.381 8.48 0.00 0.00 2.59
1792 1878 2.359900 CCTCCCAGCACAATTGTCTAC 58.640 52.381 8.48 1.22 0.00 2.59
1793 1879 2.026822 CCTCCCAGCACAATTGTCTACT 60.027 50.000 8.48 3.76 0.00 2.57
1794 1880 3.005554 CTCCCAGCACAATTGTCTACTG 58.994 50.000 19.13 19.13 0.00 2.74
1796 1882 2.744202 CCCAGCACAATTGTCTACTGTC 59.256 50.000 22.07 5.97 0.00 3.51
1797 1883 3.402110 CCAGCACAATTGTCTACTGTCA 58.598 45.455 22.07 0.00 0.00 3.58
1798 1884 3.434641 CCAGCACAATTGTCTACTGTCAG 59.565 47.826 22.07 0.00 0.00 3.51
1802 1888 4.387256 GCACAATTGTCTACTGTCAGAGTC 59.613 45.833 8.48 0.00 35.96 3.36
1808 1894 2.164624 GTCTACTGTCAGAGTCGCCATT 59.835 50.000 6.91 0.00 35.96 3.16
1832 1918 2.933495 TGCTGAATCTTGCATGCTTC 57.067 45.000 20.33 14.32 33.94 3.86
1833 1919 1.475280 TGCTGAATCTTGCATGCTTCC 59.525 47.619 20.33 3.34 33.94 3.46
1834 1920 1.749634 GCTGAATCTTGCATGCTTCCT 59.250 47.619 20.33 0.00 0.00 3.36
1837 1923 0.737219 AATCTTGCATGCTTCCTCGC 59.263 50.000 20.33 0.00 0.00 5.03
1838 1924 1.434622 ATCTTGCATGCTTCCTCGCG 61.435 55.000 20.33 0.00 0.00 5.87
1839 1925 2.047370 TTGCATGCTTCCTCGCGA 60.047 55.556 20.33 9.26 0.00 5.87
1840 1926 1.434622 CTTGCATGCTTCCTCGCGAT 61.435 55.000 20.33 0.00 0.00 4.58
1841 1927 1.026182 TTGCATGCTTCCTCGCGATT 61.026 50.000 20.33 0.00 0.00 3.34
1842 1928 1.010350 GCATGCTTCCTCGCGATTG 60.010 57.895 10.36 4.01 0.00 2.67
1843 1929 1.010350 CATGCTTCCTCGCGATTGC 60.010 57.895 10.36 12.29 37.91 3.56
1955 2044 1.375098 GCAAGGGCTAGCAGCAAGAG 61.375 60.000 18.24 0.28 44.75 2.85
2067 2160 3.022287 CCGCAGTTTGACGCTTGT 58.978 55.556 0.00 0.00 0.00 3.16
2109 2215 0.390472 CTCTCTTCTCCACGGTTGCC 60.390 60.000 0.00 0.00 0.00 4.52
2222 2332 7.386848 ACATTGGTTGTGTATTGTACTGTACTC 59.613 37.037 17.98 7.52 37.11 2.59
2240 2355 5.943416 TGTACTCTTCTCTTCTCTTCTCCAG 59.057 44.000 0.00 0.00 0.00 3.86
2242 2357 3.763360 CTCTTCTCTTCTCTTCTCCAGCA 59.237 47.826 0.00 0.00 0.00 4.41
2255 2370 0.685660 TCCAGCATTGCAATTTGGCA 59.314 45.000 25.13 15.86 43.19 4.92
2261 2376 3.004171 GCATTGCAATTTGGCATCTTCA 58.996 40.909 9.83 0.00 44.48 3.02
2266 2381 3.808726 TGCAATTTGGCATCTTCACAAAC 59.191 39.130 0.00 0.00 39.25 2.93
2270 2385 2.655090 TGGCATCTTCACAAACCTGA 57.345 45.000 0.00 0.00 0.00 3.86
2275 2390 1.808411 TCTTCACAAACCTGATCGCC 58.192 50.000 0.00 0.00 0.00 5.54
2278 2393 0.389817 TCACAAACCTGATCGCCGAG 60.390 55.000 0.00 0.00 0.00 4.63
2280 2395 1.218047 CAAACCTGATCGCCGAGGA 59.782 57.895 3.90 0.00 33.16 3.71
2286 2410 1.405526 CCTGATCGCCGAGGAAAAGAA 60.406 52.381 0.00 0.00 0.00 2.52
2299 2423 6.145535 CGAGGAAAAGAACTTCAAAAGATGG 58.854 40.000 0.00 0.00 0.00 3.51
2311 2435 7.428826 ACTTCAAAAGATGGATTTCAGTTCAC 58.571 34.615 0.00 0.00 0.00 3.18
2323 2447 1.355381 TCAGTTCACATCCAATGGCCT 59.645 47.619 3.32 0.00 33.60 5.19
2325 2449 2.684881 CAGTTCACATCCAATGGCCTAC 59.315 50.000 3.32 0.00 33.60 3.18
2326 2450 2.024414 GTTCACATCCAATGGCCTACC 58.976 52.381 3.32 0.00 33.60 3.18
2328 2452 2.770447 TCACATCCAATGGCCTACCTA 58.230 47.619 3.32 0.00 36.63 3.08
2331 2455 4.167892 TCACATCCAATGGCCTACCTAAAT 59.832 41.667 3.32 0.00 36.63 1.40
2333 2457 5.363580 CACATCCAATGGCCTACCTAAATTT 59.636 40.000 3.32 0.00 36.63 1.82
2334 2458 6.549364 CACATCCAATGGCCTACCTAAATTTA 59.451 38.462 3.32 0.00 36.63 1.40
2335 2459 7.233348 CACATCCAATGGCCTACCTAAATTTAT 59.767 37.037 3.32 0.00 36.63 1.40
2336 2460 7.451566 ACATCCAATGGCCTACCTAAATTTATC 59.548 37.037 3.32 0.00 36.63 1.75
2337 2461 7.161715 TCCAATGGCCTACCTAAATTTATCT 57.838 36.000 3.32 0.00 36.63 1.98
2341 2465 6.841781 TGGCCTACCTAAATTTATCTCCTT 57.158 37.500 3.32 0.00 36.63 3.36
2342 2466 6.838382 TGGCCTACCTAAATTTATCTCCTTC 58.162 40.000 3.32 0.00 36.63 3.46
2344 2473 6.937465 GGCCTACCTAAATTTATCTCCTTCTG 59.063 42.308 0.00 0.00 0.00 3.02
2347 2476 9.771534 CCTACCTAAATTTATCTCCTTCTGAAG 57.228 37.037 10.46 10.46 0.00 3.02
2349 2478 7.057264 ACCTAAATTTATCTCCTTCTGAAGCC 58.943 38.462 11.93 0.00 0.00 4.35
2351 2480 5.359194 AATTTATCTCCTTCTGAAGCCGA 57.641 39.130 11.93 10.00 0.00 5.54
2352 2481 4.392921 TTTATCTCCTTCTGAAGCCGAG 57.607 45.455 11.93 13.19 0.00 4.63
2354 2483 0.251832 TCTCCTTCTGAAGCCGAGGT 60.252 55.000 17.84 0.00 0.00 3.85
2373 2502 3.538614 GGCATGGCCGTCTAGAGA 58.461 61.111 8.35 0.00 39.62 3.10
2377 2506 0.309302 CATGGCCGTCTAGAGAGTCG 59.691 60.000 0.00 0.00 34.51 4.18
2422 2553 9.415544 GAAACAAGAGAATTTGTATCATTTGCT 57.584 29.630 0.00 0.00 40.24 3.91
2423 2554 8.752766 AACAAGAGAATTTGTATCATTTGCTG 57.247 30.769 0.00 0.00 40.24 4.41
2425 2556 8.579006 ACAAGAGAATTTGTATCATTTGCTGAA 58.421 29.630 0.00 0.00 39.40 3.02
2426 2557 8.857216 CAAGAGAATTTGTATCATTTGCTGAAC 58.143 33.333 0.00 0.00 37.44 3.18
2430 2561 9.415544 AGAATTTGTATCATTTGCTGAACTTTC 57.584 29.630 0.00 0.00 37.44 2.62
2431 2562 9.195411 GAATTTGTATCATTTGCTGAACTTTCA 57.805 29.630 0.00 0.00 37.44 2.69
2433 2564 8.746922 TTTGTATCATTTGCTGAACTTTCATC 57.253 30.769 0.00 0.00 37.44 2.92
2437 2568 6.169419 TCATTTGCTGAACTTTCATCGTAG 57.831 37.500 0.00 0.00 36.46 3.51
2439 2570 5.591643 TTTGCTGAACTTTCATCGTAGAC 57.408 39.130 0.00 0.00 42.51 2.59
2441 2572 4.627058 TGCTGAACTTTCATCGTAGACAA 58.373 39.130 0.00 0.00 42.51 3.18
2443 2574 5.525745 TGCTGAACTTTCATCGTAGACAAAA 59.474 36.000 0.00 0.00 42.51 2.44
2444 2575 6.037720 TGCTGAACTTTCATCGTAGACAAAAA 59.962 34.615 0.00 0.00 42.51 1.94
2468 2612 0.401738 TGAGAAGGTCAGCCAAAGGG 59.598 55.000 0.00 0.00 37.19 3.95
2482 2626 0.037447 AAAGGGGCTCTCTGTGCTTC 59.963 55.000 0.00 0.00 0.00 3.86
2516 2660 1.000060 TGTCCTGAAAATGCAAGCAGC 60.000 47.619 0.00 0.00 45.96 5.25
2582 2731 4.397420 TGTGACTTACAATTGCCTGATGT 58.603 39.130 5.05 0.00 36.06 3.06
2585 2734 5.643777 GTGACTTACAATTGCCTGATGTAGT 59.356 40.000 5.05 0.00 31.72 2.73
2586 2735 6.149474 GTGACTTACAATTGCCTGATGTAGTT 59.851 38.462 5.05 0.00 31.72 2.24
2588 2737 7.230510 TGACTTACAATTGCCTGATGTAGTTTT 59.769 33.333 5.05 0.00 31.72 2.43
2590 2739 9.243105 ACTTACAATTGCCTGATGTAGTTTTAT 57.757 29.630 5.05 0.00 31.72 1.40
2593 2742 8.121305 ACAATTGCCTGATGTAGTTTTATTCA 57.879 30.769 5.05 0.00 0.00 2.57
2594 2743 8.246180 ACAATTGCCTGATGTAGTTTTATTCAG 58.754 33.333 5.05 0.00 0.00 3.02
2595 2744 6.757897 TTGCCTGATGTAGTTTTATTCAGG 57.242 37.500 11.92 11.92 44.25 3.86
2600 2749 6.998074 CCTGATGTAGTTTTATTCAGGCCATA 59.002 38.462 5.01 0.00 37.13 2.74
2602 2751 8.220755 TGATGTAGTTTTATTCAGGCCATAAC 57.779 34.615 5.01 0.00 0.00 1.89
2603 2752 7.831690 TGATGTAGTTTTATTCAGGCCATAACA 59.168 33.333 5.01 0.00 0.00 2.41
2604 2753 8.766994 ATGTAGTTTTATTCAGGCCATAACAT 57.233 30.769 5.01 0.00 0.00 2.71
2605 2754 9.860650 ATGTAGTTTTATTCAGGCCATAACATA 57.139 29.630 5.01 0.00 0.00 2.29
2606 2755 9.860650 TGTAGTTTTATTCAGGCCATAACATAT 57.139 29.630 5.01 0.00 0.00 1.78
2610 2759 9.683069 GTTTTATTCAGGCCATAACATATTCTG 57.317 33.333 5.01 0.00 0.00 3.02
2611 2760 8.995027 TTTATTCAGGCCATAACATATTCTGT 57.005 30.769 5.01 0.00 40.84 3.41
2612 2761 6.889301 ATTCAGGCCATAACATATTCTGTG 57.111 37.500 5.01 0.00 38.39 3.66
2613 2762 4.717877 TCAGGCCATAACATATTCTGTGG 58.282 43.478 5.01 0.00 38.39 4.17
2614 2763 3.254166 CAGGCCATAACATATTCTGTGGC 59.746 47.826 5.01 11.31 41.50 5.01
2615 2764 3.117550 AGGCCATAACATATTCTGTGGCA 60.118 43.478 18.10 0.00 43.13 4.92
2616 2765 3.636300 GGCCATAACATATTCTGTGGCAA 59.364 43.478 18.10 0.00 43.13 4.52
2617 2766 4.281688 GGCCATAACATATTCTGTGGCAAT 59.718 41.667 18.10 0.00 43.13 3.56
2618 2767 5.224888 GCCATAACATATTCTGTGGCAATG 58.775 41.667 13.75 0.00 41.72 2.82
2619 2768 5.775686 CCATAACATATTCTGTGGCAATGG 58.224 41.667 0.00 0.00 38.39 3.16
2620 2769 5.302568 CCATAACATATTCTGTGGCAATGGT 59.697 40.000 0.00 0.00 38.39 3.55
2621 2770 6.183360 CCATAACATATTCTGTGGCAATGGTT 60.183 38.462 0.00 0.00 38.39 3.67
2622 2771 5.743636 AACATATTCTGTGGCAATGGTTT 57.256 34.783 0.00 0.00 38.39 3.27
2623 2772 5.743636 ACATATTCTGTGGCAATGGTTTT 57.256 34.783 0.00 0.00 36.48 2.43
2624 2773 6.849085 ACATATTCTGTGGCAATGGTTTTA 57.151 33.333 0.00 0.00 36.48 1.52
2631 2780 3.756434 TGTGGCAATGGTTTTAGTAGAGC 59.244 43.478 0.00 0.00 0.00 4.09
2634 2783 4.830046 TGGCAATGGTTTTAGTAGAGCAAA 59.170 37.500 0.00 0.00 0.00 3.68
2695 2845 1.500512 TACAAGAACACGCAACGGCC 61.501 55.000 0.00 0.00 36.38 6.13
2757 2907 5.994054 CACAGACCCACAATATCAATAGGAG 59.006 44.000 0.00 0.00 0.00 3.69
2828 2984 9.231297 CTTCATTTATTTATCCGGGTATCACAT 57.769 33.333 0.00 0.00 0.00 3.21
2890 3046 2.098614 TGTATGGTCCGCCGTAAAGTA 58.901 47.619 0.00 0.00 37.94 2.24
2918 3074 2.028020 CACTACCAGGGTTCAGGTCTTC 60.028 54.545 0.00 0.00 39.31 2.87
2978 3141 3.851458 AACCGACTCTTAACCACCTTT 57.149 42.857 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.207329 ACCGCTATCTGACAAGTTCCC 59.793 52.381 0.00 0.00 0.00 3.97
1 2 2.673368 CAACCGCTATCTGACAAGTTCC 59.327 50.000 0.00 0.00 0.00 3.62
2 3 3.123621 CACAACCGCTATCTGACAAGTTC 59.876 47.826 0.00 0.00 0.00 3.01
3 4 3.067106 CACAACCGCTATCTGACAAGTT 58.933 45.455 0.00 0.00 0.00 2.66
4 5 2.299013 TCACAACCGCTATCTGACAAGT 59.701 45.455 0.00 0.00 0.00 3.16
5 6 2.959516 TCACAACCGCTATCTGACAAG 58.040 47.619 0.00 0.00 0.00 3.16
6 7 3.261580 CATCACAACCGCTATCTGACAA 58.738 45.455 0.00 0.00 0.00 3.18
7 8 2.418609 CCATCACAACCGCTATCTGACA 60.419 50.000 0.00 0.00 0.00 3.58
8 9 2.205074 CCATCACAACCGCTATCTGAC 58.795 52.381 0.00 0.00 0.00 3.51
9 10 1.473257 GCCATCACAACCGCTATCTGA 60.473 52.381 0.00 0.00 0.00 3.27
10 11 0.940126 GCCATCACAACCGCTATCTG 59.060 55.000 0.00 0.00 0.00 2.90
11 12 0.179045 GGCCATCACAACCGCTATCT 60.179 55.000 0.00 0.00 0.00 1.98
12 13 1.498865 CGGCCATCACAACCGCTATC 61.499 60.000 2.24 0.00 40.55 2.08
13 14 1.523711 CGGCCATCACAACCGCTAT 60.524 57.895 2.24 0.00 40.55 2.97
14 15 2.125310 CGGCCATCACAACCGCTA 60.125 61.111 2.24 0.00 40.55 4.26
17 18 2.124736 ATCCGGCCATCACAACCG 60.125 61.111 2.24 0.00 46.50 4.44
18 19 2.180204 CGATCCGGCCATCACAACC 61.180 63.158 2.24 0.00 0.00 3.77
19 20 1.449601 ACGATCCGGCCATCACAAC 60.450 57.895 2.24 0.00 0.00 3.32
20 21 1.449423 CACGATCCGGCCATCACAA 60.449 57.895 2.24 0.00 0.00 3.33
21 22 2.186644 CACGATCCGGCCATCACA 59.813 61.111 2.24 0.00 0.00 3.58
22 23 3.272334 GCACGATCCGGCCATCAC 61.272 66.667 2.24 0.00 0.00 3.06
23 24 4.889856 CGCACGATCCGGCCATCA 62.890 66.667 2.24 0.00 0.00 3.07
48 49 2.435586 ACACATCGAGCAGCTGGC 60.436 61.111 17.12 7.98 45.30 4.85
49 50 1.812922 GGACACATCGAGCAGCTGG 60.813 63.158 17.12 0.00 0.00 4.85
50 51 0.671472 TTGGACACATCGAGCAGCTG 60.671 55.000 10.11 10.11 0.00 4.24
51 52 0.035317 TTTGGACACATCGAGCAGCT 59.965 50.000 0.00 0.00 0.00 4.24
52 53 1.089920 ATTTGGACACATCGAGCAGC 58.910 50.000 0.00 0.00 0.00 5.25
53 54 3.308053 CACTATTTGGACACATCGAGCAG 59.692 47.826 0.00 0.00 0.00 4.24
54 55 3.261580 CACTATTTGGACACATCGAGCA 58.738 45.455 0.00 0.00 0.00 4.26
55 56 2.030946 GCACTATTTGGACACATCGAGC 59.969 50.000 0.00 0.00 0.00 5.03
56 57 2.282555 CGCACTATTTGGACACATCGAG 59.717 50.000 0.00 0.00 0.00 4.04
57 58 2.267426 CGCACTATTTGGACACATCGA 58.733 47.619 0.00 0.00 0.00 3.59
58 59 1.999735 ACGCACTATTTGGACACATCG 59.000 47.619 0.00 0.00 0.00 3.84
59 60 4.552767 GCATACGCACTATTTGGACACATC 60.553 45.833 0.00 0.00 38.36 3.06
60 61 3.312421 GCATACGCACTATTTGGACACAT 59.688 43.478 0.00 0.00 38.36 3.21
61 62 2.675844 GCATACGCACTATTTGGACACA 59.324 45.455 0.00 0.00 38.36 3.72
62 63 2.675844 TGCATACGCACTATTTGGACAC 59.324 45.455 0.00 0.00 45.36 3.67
63 64 2.979240 TGCATACGCACTATTTGGACA 58.021 42.857 0.00 0.00 45.36 4.02
75 76 8.614994 ACATAAAATCTAAAAAGTGCATACGC 57.385 30.769 0.00 0.00 39.24 4.42
105 106 8.410141 GCATATGGGTGCTTAGTTTGTTTATTA 58.590 33.333 4.56 0.00 41.82 0.98
106 107 7.093552 TGCATATGGGTGCTTAGTTTGTTTATT 60.094 33.333 4.56 0.00 45.27 1.40
107 108 6.379703 TGCATATGGGTGCTTAGTTTGTTTAT 59.620 34.615 4.56 0.00 45.27 1.40
108 109 5.712446 TGCATATGGGTGCTTAGTTTGTTTA 59.288 36.000 4.56 0.00 45.27 2.01
109 110 4.526262 TGCATATGGGTGCTTAGTTTGTTT 59.474 37.500 4.56 0.00 45.27 2.83
110 111 4.085733 TGCATATGGGTGCTTAGTTTGTT 58.914 39.130 4.56 0.00 45.27 2.83
111 112 3.696045 TGCATATGGGTGCTTAGTTTGT 58.304 40.909 4.56 0.00 45.27 2.83
112 113 4.613944 CATGCATATGGGTGCTTAGTTTG 58.386 43.478 0.00 0.00 45.27 2.93
113 114 3.068590 GCATGCATATGGGTGCTTAGTTT 59.931 43.478 14.21 0.00 45.27 2.66
114 115 2.624838 GCATGCATATGGGTGCTTAGTT 59.375 45.455 14.21 0.00 45.27 2.24
115 116 2.233271 GCATGCATATGGGTGCTTAGT 58.767 47.619 14.21 0.00 45.27 2.24
116 117 1.198408 CGCATGCATATGGGTGCTTAG 59.802 52.381 19.57 0.00 45.27 2.18
117 118 1.237533 CGCATGCATATGGGTGCTTA 58.762 50.000 19.57 0.00 45.27 3.09
118 119 2.035421 CGCATGCATATGGGTGCTT 58.965 52.632 19.57 0.00 45.27 3.91
119 120 3.754068 CGCATGCATATGGGTGCT 58.246 55.556 19.57 0.00 45.27 4.40
124 125 2.847959 TGTGAAACGCATGCATATGG 57.152 45.000 19.57 2.94 42.39 2.74
125 126 5.512573 TTTTTGTGAAACGCATGCATATG 57.487 34.783 19.57 3.36 42.39 1.78
126 127 5.868258 TCATTTTTGTGAAACGCATGCATAT 59.132 32.000 19.57 1.64 42.39 1.78
127 128 5.225642 TCATTTTTGTGAAACGCATGCATA 58.774 33.333 19.57 0.00 42.39 3.14
133 134 7.436376 TCATGTTTATCATTTTTGTGAAACGCA 59.564 29.630 0.00 0.00 35.04 5.24
155 156 4.670896 AAGAAAAAGGGTTGGTGTCATG 57.329 40.909 0.00 0.00 0.00 3.07
167 168 5.569059 GCATATGACGTGACAAAGAAAAAGG 59.431 40.000 6.97 0.00 0.00 3.11
169 170 5.143660 CGCATATGACGTGACAAAGAAAAA 58.856 37.500 6.97 0.00 0.00 1.94
195 200 2.096218 GCTTTCTCATCACCGTGTGAAC 60.096 50.000 10.17 0.00 45.96 3.18
236 242 4.521943 GAATGATGATGCTACTTGCGTTC 58.478 43.478 0.00 0.00 46.63 3.95
254 260 1.033746 AGGAATGCACGGCAGGAATG 61.034 55.000 0.00 0.00 43.65 2.67
255 261 0.749454 GAGGAATGCACGGCAGGAAT 60.749 55.000 0.00 0.00 43.65 3.01
256 262 1.377202 GAGGAATGCACGGCAGGAA 60.377 57.895 0.00 0.00 43.65 3.36
259 265 2.046023 TGGAGGAATGCACGGCAG 60.046 61.111 0.00 0.00 43.65 4.85
260 266 2.359850 GTGGAGGAATGCACGGCA 60.360 61.111 0.00 1.01 44.86 5.69
261 267 3.499737 CGTGGAGGAATGCACGGC 61.500 66.667 13.50 0.00 37.40 5.68
262 268 3.499737 GCGTGGAGGAATGCACGG 61.500 66.667 20.88 6.04 40.85 4.94
263 269 3.853330 CGCGTGGAGGAATGCACG 61.853 66.667 16.42 16.42 43.04 5.34
264 270 2.740714 GACGCGTGGAGGAATGCAC 61.741 63.158 20.70 0.00 32.08 4.57
265 271 2.434185 GACGCGTGGAGGAATGCA 60.434 61.111 20.70 0.00 32.08 3.96
266 272 2.434185 TGACGCGTGGAGGAATGC 60.434 61.111 20.70 0.00 0.00 3.56
267 273 2.444624 CGTGACGCGTGGAGGAATG 61.445 63.158 20.70 0.00 35.54 2.67
268 274 2.126071 CGTGACGCGTGGAGGAAT 60.126 61.111 20.70 0.00 35.54 3.01
287 293 2.033236 CGGCACATATTCGCATAACGTT 60.033 45.455 5.88 5.88 44.19 3.99
345 359 1.734359 TTTGCGTTGCGTTGCGTTTC 61.734 50.000 0.00 0.00 0.00 2.78
349 363 2.534234 CTTTTGCGTTGCGTTGCG 59.466 55.556 0.00 0.00 0.00 4.85
350 364 2.242386 GCTTTTGCGTTGCGTTGC 59.758 55.556 0.00 0.00 34.86 4.17
361 375 5.736358 GTGATAAATCTCGAGCTTGCTTTTG 59.264 40.000 7.81 0.00 0.00 2.44
362 376 5.446473 CGTGATAAATCTCGAGCTTGCTTTT 60.446 40.000 7.81 3.51 43.97 2.27
363 377 4.033358 CGTGATAAATCTCGAGCTTGCTTT 59.967 41.667 7.81 5.00 43.97 3.51
364 378 3.553511 CGTGATAAATCTCGAGCTTGCTT 59.446 43.478 7.81 0.00 43.97 3.91
365 379 3.119291 CGTGATAAATCTCGAGCTTGCT 58.881 45.455 7.81 0.00 43.97 3.91
366 380 2.860735 ACGTGATAAATCTCGAGCTTGC 59.139 45.455 18.19 0.00 43.97 4.01
367 381 3.859961 ACACGTGATAAATCTCGAGCTTG 59.140 43.478 25.01 10.02 43.97 4.01
368 382 4.111375 ACACGTGATAAATCTCGAGCTT 57.889 40.909 25.01 0.41 43.97 3.74
381 395 2.230266 GGGGCAAAAACATACACGTGAT 59.770 45.455 25.01 8.63 0.00 3.06
390 404 4.450976 GAGACAAAAAGGGGCAAAAACAT 58.549 39.130 0.00 0.00 0.00 2.71
391 405 3.677424 CGAGACAAAAAGGGGCAAAAACA 60.677 43.478 0.00 0.00 0.00 2.83
398 412 1.807142 CTCTTCGAGACAAAAAGGGGC 59.193 52.381 0.00 0.00 0.00 5.80
425 442 2.983592 CCACGCCACCAACCTTCC 60.984 66.667 0.00 0.00 0.00 3.46
426 443 2.983592 CCCACGCCACCAACCTTC 60.984 66.667 0.00 0.00 0.00 3.46
431 448 2.034999 GATTCCCCACGCCACCAA 59.965 61.111 0.00 0.00 0.00 3.67
432 449 4.402528 CGATTCCCCACGCCACCA 62.403 66.667 0.00 0.00 0.00 4.17
944 964 2.603652 AACGGGAGGGAAGGGAAGC 61.604 63.158 0.00 0.00 0.00 3.86
945 965 1.299976 CAACGGGAGGGAAGGGAAG 59.700 63.158 0.00 0.00 0.00 3.46
946 966 2.902457 GCAACGGGAGGGAAGGGAA 61.902 63.158 0.00 0.00 0.00 3.97
947 967 3.327404 GCAACGGGAGGGAAGGGA 61.327 66.667 0.00 0.00 0.00 4.20
948 968 3.330720 AGCAACGGGAGGGAAGGG 61.331 66.667 0.00 0.00 0.00 3.95
949 969 2.269241 GAGCAACGGGAGGGAAGG 59.731 66.667 0.00 0.00 0.00 3.46
979 1037 1.664588 GCAGATGTAGATCGGACGAGC 60.665 57.143 4.16 1.18 33.34 5.03
992 1050 0.043940 AGAGAGAAGGGGGCAGATGT 59.956 55.000 0.00 0.00 0.00 3.06
1020 1084 4.515432 CGAGAACGAAGGAAGAAAAACAC 58.485 43.478 0.00 0.00 42.66 3.32
1021 1085 3.558418 CCGAGAACGAAGGAAGAAAAACA 59.442 43.478 0.00 0.00 42.66 2.83
1316 1388 1.077429 AGCAAAGGAGCGGGAATCC 60.077 57.895 0.00 0.00 40.15 3.01
1317 1389 1.432270 CGAGCAAAGGAGCGGGAATC 61.432 60.000 0.00 0.00 40.15 2.52
1319 1391 2.047274 CGAGCAAAGGAGCGGGAA 60.047 61.111 0.00 0.00 40.15 3.97
1320 1392 4.760047 GCGAGCAAAGGAGCGGGA 62.760 66.667 0.00 0.00 40.15 5.14
1328 1402 1.735920 AGTCAGCGAGCGAGCAAAG 60.736 57.895 9.01 0.00 40.15 2.77
1627 1713 1.144276 GTAGGCCTTCTTCCGCTCC 59.856 63.158 12.58 0.00 0.00 4.70
1791 1877 0.671781 GCAATGGCGACTCTGACAGT 60.672 55.000 1.59 0.00 38.45 3.55
1792 1878 2.084844 GCAATGGCGACTCTGACAG 58.915 57.895 0.00 0.00 0.00 3.51
1793 1879 4.284123 GCAATGGCGACTCTGACA 57.716 55.556 0.00 0.00 0.00 3.58
1808 1894 2.857254 TGCAAGATTCAGCATCGCA 58.143 47.368 0.34 0.00 36.93 5.10
1814 1900 1.749634 AGGAAGCATGCAAGATTCAGC 59.250 47.619 21.98 5.34 35.70 4.26
1837 1923 0.578683 CAGTATCTGCACCGCAATCG 59.421 55.000 0.00 0.00 38.41 3.34
1838 1924 1.939974 TCAGTATCTGCACCGCAATC 58.060 50.000 0.00 0.00 38.41 2.67
1839 1925 2.093500 TCTTCAGTATCTGCACCGCAAT 60.093 45.455 0.00 0.00 38.41 3.56
1840 1926 1.275010 TCTTCAGTATCTGCACCGCAA 59.725 47.619 0.00 0.00 38.41 4.85
1841 1927 0.894835 TCTTCAGTATCTGCACCGCA 59.105 50.000 0.00 0.00 36.92 5.69
1842 1928 1.661112 GTTCTTCAGTATCTGCACCGC 59.339 52.381 0.00 0.00 0.00 5.68
1843 1929 2.668457 GTGTTCTTCAGTATCTGCACCG 59.332 50.000 0.00 0.00 0.00 4.94
1844 1930 2.668457 CGTGTTCTTCAGTATCTGCACC 59.332 50.000 0.00 0.00 0.00 5.01
2067 2160 6.653989 AGGAGTGAAAAAGAAGAAGACAAGA 58.346 36.000 0.00 0.00 0.00 3.02
2222 2332 4.741321 ATGCTGGAGAAGAGAAGAGAAG 57.259 45.455 0.00 0.00 0.00 2.85
2240 2355 3.004171 TGAAGATGCCAAATTGCAATGC 58.996 40.909 13.82 12.81 45.84 3.56
2242 2357 4.274602 TGTGAAGATGCCAAATTGCAAT 57.725 36.364 5.99 5.99 45.84 3.56
2255 2370 2.359900 GGCGATCAGGTTTGTGAAGAT 58.640 47.619 0.00 0.00 0.00 2.40
2261 2376 1.079127 CCTCGGCGATCAGGTTTGT 60.079 57.895 11.27 0.00 0.00 2.83
2266 2381 0.175760 TCTTTTCCTCGGCGATCAGG 59.824 55.000 11.27 8.95 0.00 3.86
2270 2385 2.289444 TGAAGTTCTTTTCCTCGGCGAT 60.289 45.455 11.27 0.00 0.00 4.58
2275 2390 6.017109 TCCATCTTTTGAAGTTCTTTTCCTCG 60.017 38.462 4.17 0.00 0.00 4.63
2278 2393 8.893219 AAATCCATCTTTTGAAGTTCTTTTCC 57.107 30.769 4.17 0.00 0.00 3.13
2280 2395 9.538508 CTGAAATCCATCTTTTGAAGTTCTTTT 57.461 29.630 4.17 0.00 0.00 2.27
2286 2410 7.068593 TGTGAACTGAAATCCATCTTTTGAAGT 59.931 33.333 0.00 0.00 0.00 3.01
2299 2423 4.427312 GCCATTGGATGTGAACTGAAATC 58.573 43.478 6.95 0.00 0.00 2.17
2311 2435 7.671398 AGATAAATTTAGGTAGGCCATTGGATG 59.329 37.037 5.01 0.00 37.19 3.51
2316 2440 7.408013 AGGAGATAAATTTAGGTAGGCCATT 57.592 36.000 5.01 0.00 37.19 3.16
2323 2447 8.211629 GGCTTCAGAAGGAGATAAATTTAGGTA 58.788 37.037 12.30 0.00 0.00 3.08
2325 2449 6.203723 CGGCTTCAGAAGGAGATAAATTTAGG 59.796 42.308 12.30 0.00 0.00 2.69
2326 2450 6.986817 TCGGCTTCAGAAGGAGATAAATTTAG 59.013 38.462 12.30 0.00 0.00 1.85
2328 2452 5.745227 TCGGCTTCAGAAGGAGATAAATTT 58.255 37.500 12.30 0.00 0.00 1.82
2331 2455 3.133003 CCTCGGCTTCAGAAGGAGATAAA 59.867 47.826 12.30 0.00 0.00 1.40
2333 2457 2.311463 CCTCGGCTTCAGAAGGAGATA 58.689 52.381 12.30 0.00 0.00 1.98
2334 2458 1.118838 CCTCGGCTTCAGAAGGAGAT 58.881 55.000 12.30 0.00 0.00 2.75
2335 2459 0.251832 ACCTCGGCTTCAGAAGGAGA 60.252 55.000 12.30 0.00 0.00 3.71
2336 2460 1.407258 CTACCTCGGCTTCAGAAGGAG 59.593 57.143 12.30 10.23 0.00 3.69
2337 2461 1.475403 CTACCTCGGCTTCAGAAGGA 58.525 55.000 12.30 0.96 0.00 3.36
2341 2465 3.617368 GCCTACCTCGGCTTCAGA 58.383 61.111 0.00 0.00 46.63 3.27
2360 2489 4.220413 CGACTCTCTAGACGGCCA 57.780 61.111 2.24 0.00 37.27 5.36
2366 2495 2.036862 TGCTATACGCCGACTCTCTAGA 59.963 50.000 0.00 0.00 38.05 2.43
2367 2496 2.413796 CTGCTATACGCCGACTCTCTAG 59.586 54.545 0.00 0.00 38.05 2.43
2369 2498 1.231221 CTGCTATACGCCGACTCTCT 58.769 55.000 0.00 0.00 38.05 3.10
2373 2502 1.101635 TCAGCTGCTATACGCCGACT 61.102 55.000 9.47 0.00 38.05 4.18
2377 2506 1.143305 CACATCAGCTGCTATACGCC 58.857 55.000 9.47 0.00 38.05 5.68
2389 2520 9.552114 GATACAAATTCTCTTGTTTCACATCAG 57.448 33.333 0.00 0.00 40.08 2.90
2395 2526 9.195411 GCAAATGATACAAATTCTCTTGTTTCA 57.805 29.630 10.57 10.57 45.24 2.69
2398 2529 8.579006 TCAGCAAATGATACAAATTCTCTTGTT 58.421 29.630 0.00 0.00 35.53 2.83
2399 2530 8.114331 TCAGCAAATGATACAAATTCTCTTGT 57.886 30.769 0.00 0.00 36.86 3.16
2403 2534 8.976986 AAGTTCAGCAAATGATACAAATTCTC 57.023 30.769 0.00 0.00 37.89 2.87
2406 2537 9.715121 ATGAAAGTTCAGCAAATGATACAAATT 57.285 25.926 0.00 0.00 41.08 1.82
2407 2538 9.362539 GATGAAAGTTCAGCAAATGATACAAAT 57.637 29.630 4.48 0.00 42.78 2.32
2411 2542 6.546395 ACGATGAAAGTTCAGCAAATGATAC 58.454 36.000 9.71 0.00 43.38 2.24
2415 2546 6.017933 GTCTACGATGAAAGTTCAGCAAATG 58.982 40.000 9.71 0.00 43.38 2.32
2443 2574 1.494721 TGGCTGACCTTCTCACCTTTT 59.505 47.619 0.00 0.00 36.63 2.27
2444 2575 1.140312 TGGCTGACCTTCTCACCTTT 58.860 50.000 0.00 0.00 36.63 3.11
2445 2576 1.140312 TTGGCTGACCTTCTCACCTT 58.860 50.000 0.00 0.00 36.63 3.50
2446 2577 1.072965 CTTTGGCTGACCTTCTCACCT 59.927 52.381 0.00 0.00 36.63 4.00
2448 2579 1.528129 CCTTTGGCTGACCTTCTCAC 58.472 55.000 0.00 0.00 36.63 3.51
2449 2580 0.401738 CCCTTTGGCTGACCTTCTCA 59.598 55.000 0.00 0.00 36.63 3.27
2450 2581 0.322906 CCCCTTTGGCTGACCTTCTC 60.323 60.000 0.00 0.00 36.63 2.87
2451 2582 1.770324 CCCCTTTGGCTGACCTTCT 59.230 57.895 0.00 0.00 36.63 2.85
2468 2612 0.319900 TTGACGAAGCACAGAGAGCC 60.320 55.000 0.00 0.00 0.00 4.70
2473 2617 2.899976 TGTTCTTTGACGAAGCACAGA 58.100 42.857 4.02 0.00 36.74 3.41
2482 2626 1.528586 CAGGACAGCTGTTCTTTGACG 59.471 52.381 25.72 9.98 29.58 4.35
2531 2675 3.198863 CAGCTGTTCTGAATTCAGTGC 57.801 47.619 29.80 26.23 45.72 4.40
2560 2704 4.397420 ACATCAGGCAATTGTAAGTCACA 58.603 39.130 7.40 0.00 34.51 3.58
2561 2710 5.643777 ACTACATCAGGCAATTGTAAGTCAC 59.356 40.000 7.40 0.00 0.00 3.67
2585 2734 9.420118 ACAGAATATGTTATGGCCTGAATAAAA 57.580 29.630 3.32 0.00 39.96 1.52
2586 2735 8.849168 CACAGAATATGTTATGGCCTGAATAAA 58.151 33.333 3.32 0.00 41.41 1.40
2588 2737 6.942005 CCACAGAATATGTTATGGCCTGAATA 59.058 38.462 3.32 0.00 41.41 1.75
2590 2739 5.132502 CCACAGAATATGTTATGGCCTGAA 58.867 41.667 3.32 0.00 41.41 3.02
2591 2740 4.717877 CCACAGAATATGTTATGGCCTGA 58.282 43.478 3.32 0.00 41.41 3.86
2592 2741 3.254166 GCCACAGAATATGTTATGGCCTG 59.746 47.826 3.32 0.00 40.82 4.85
2593 2742 3.117550 TGCCACAGAATATGTTATGGCCT 60.118 43.478 16.91 0.00 44.24 5.19
2594 2743 3.221771 TGCCACAGAATATGTTATGGCC 58.778 45.455 16.91 0.00 44.24 5.36
2595 2744 4.916983 TTGCCACAGAATATGTTATGGC 57.083 40.909 14.25 14.25 44.80 4.40
2600 2749 5.743636 AAACCATTGCCACAGAATATGTT 57.256 34.783 0.00 0.00 41.41 2.71
2602 2751 6.866480 ACTAAAACCATTGCCACAGAATATG 58.134 36.000 0.00 0.00 0.00 1.78
2603 2752 8.052748 TCTACTAAAACCATTGCCACAGAATAT 58.947 33.333 0.00 0.00 0.00 1.28
2604 2753 7.398829 TCTACTAAAACCATTGCCACAGAATA 58.601 34.615 0.00 0.00 0.00 1.75
2605 2754 6.245408 TCTACTAAAACCATTGCCACAGAAT 58.755 36.000 0.00 0.00 0.00 2.40
2606 2755 5.626142 TCTACTAAAACCATTGCCACAGAA 58.374 37.500 0.00 0.00 0.00 3.02
2608 2757 4.142600 GCTCTACTAAAACCATTGCCACAG 60.143 45.833 0.00 0.00 0.00 3.66
2610 2759 3.756434 TGCTCTACTAAAACCATTGCCAC 59.244 43.478 0.00 0.00 0.00 5.01
2611 2760 4.027674 TGCTCTACTAAAACCATTGCCA 57.972 40.909 0.00 0.00 0.00 4.92
2612 2761 5.385509 TTTGCTCTACTAAAACCATTGCC 57.614 39.130 0.00 0.00 0.00 4.52
2613 2762 7.062255 GTCAATTTGCTCTACTAAAACCATTGC 59.938 37.037 0.00 0.00 0.00 3.56
2614 2763 8.299570 AGTCAATTTGCTCTACTAAAACCATTG 58.700 33.333 0.00 0.00 0.00 2.82
2615 2764 8.409358 AGTCAATTTGCTCTACTAAAACCATT 57.591 30.769 0.00 0.00 0.00 3.16
2616 2765 8.299570 CAAGTCAATTTGCTCTACTAAAACCAT 58.700 33.333 0.00 0.00 0.00 3.55
2617 2766 7.648142 CAAGTCAATTTGCTCTACTAAAACCA 58.352 34.615 0.00 0.00 0.00 3.67
2647 2796 3.057245 GTCATTCTTTTTCCCCTCTGCAC 60.057 47.826 0.00 0.00 0.00 4.57
2654 2803 7.666623 TGTAAATTCTGTCATTCTTTTTCCCC 58.333 34.615 0.00 0.00 0.00 4.81
2695 2845 0.592637 TGCCAAGCATGAACAGAACG 59.407 50.000 0.00 0.00 31.71 3.95
2757 2907 3.403558 GGTCCCCTCCCTGACTGC 61.404 72.222 0.00 0.00 0.00 4.40
2798 2948 4.583073 ACCCGGATAAATAAATGAAGTGGC 59.417 41.667 0.73 0.00 0.00 5.01
2828 2984 6.770785 GGGCTTGGTAATTTGATGATGTACTA 59.229 38.462 0.00 0.00 0.00 1.82
2847 3003 2.209273 CCGAAAAAGTTTTGGGGCTTG 58.791 47.619 0.61 0.00 40.87 4.01
2890 3046 1.125711 AACCCTGGTAGTGGTCGCTT 61.126 55.000 0.00 0.00 32.40 4.68
2897 3053 1.645710 AGACCTGAACCCTGGTAGTG 58.354 55.000 0.00 0.00 43.54 2.74
2918 3074 8.248945 TGAAGAAAGTAGTTCGTTAAGGATAGG 58.751 37.037 0.00 0.00 41.52 2.57
2978 3141 3.897239 TGTTCTGAAGGAAAAGGCTGAA 58.103 40.909 0.00 0.00 35.51 3.02


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

AutoCloner maintained by Alex Coulton.