Multiple sequence alignment - TraesCS4D01G195000

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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 TraesCS4D01G195000 chr4D 100.000 4856 0 0 1 4856 338365523 338370378 0.000000e+00 8968
1 TraesCS4D01G195000 chr4D 93.849 634 32 3 4224 4856 37261763 37261136 0.000000e+00 948
2 TraesCS4D01G195000 chr4D 82.915 199 32 2 2565 2762 188963058 188963255 1.390000e-40 178
3 TraesCS4D01G195000 chr4D 87.705 122 15 0 1695 1816 146029041 146028920 5.070000e-30 143
4 TraesCS4D01G195000 chr4B 92.591 2065 67 28 5 2015 417349382 417351414 0.000000e+00 2887
5 TraesCS4D01G195000 chr4B 93.126 931 34 13 3191 4099 417352568 417353490 0.000000e+00 1338
6 TraesCS4D01G195000 chr4B 94.822 618 27 2 4239 4856 64814944 64814332 0.000000e+00 959
7 TraesCS4D01G195000 chr4B 91.641 323 9 4 2858 3162 417352250 417352572 9.660000e-117 431
8 TraesCS4D01G195000 chr4B 95.816 239 8 1 2232 2470 417351611 417351847 7.620000e-103 385
9 TraesCS4D01G195000 chr4B 98.585 212 3 0 2561 2772 417351919 417352130 4.590000e-100 375
10 TraesCS4D01G195000 chr4A 91.675 2006 83 36 4 1957 133844335 133842362 0.000000e+00 2702
11 TraesCS4D01G195000 chr4A 91.544 745 29 17 3466 4204 133840658 133839942 0.000000e+00 996
12 TraesCS4D01G195000 chr4A 92.429 634 23 11 2858 3472 133841337 133840710 0.000000e+00 881
13 TraesCS4D01G195000 chr4A 91.536 638 19 23 2218 2850 133841987 133841380 0.000000e+00 846
14 TraesCS4D01G195000 chr3D 95.008 621 25 2 4236 4856 156247830 156248444 0.000000e+00 970
15 TraesCS4D01G195000 chr3D 94.992 619 27 1 4236 4854 330686056 330685442 0.000000e+00 968
16 TraesCS4D01G195000 chr3D 94.686 621 26 3 4236 4856 90195443 90194830 0.000000e+00 957
17 TraesCS4D01G195000 chr3B 94.313 633 31 3 4225 4856 267006754 267006126 0.000000e+00 965
18 TraesCS4D01G195000 chr3B 83.085 201 28 5 2563 2760 602584637 602584834 1.390000e-40 178
19 TraesCS4D01G195000 chr3B 86.957 115 15 0 2275 2389 602584148 602584262 3.940000e-26 130
20 TraesCS4D01G195000 chr2D 94.304 632 28 3 4225 4855 424669562 424670186 0.000000e+00 961
21 TraesCS4D01G195000 chr2D 83.254 209 33 2 2565 2772 36535426 36535633 1.780000e-44 191
22 TraesCS4D01G195000 chr2D 87.261 157 17 2 2274 2427 36535234 36535390 5.000000e-40 176
23 TraesCS4D01G195000 chr2D 81.731 208 36 2 2565 2771 288163014 288162808 6.460000e-39 172
24 TraesCS4D01G195000 chr2D 86.957 115 15 0 2905 3019 36535729 36535843 3.940000e-26 130
25 TraesCS4D01G195000 chr5B 94.146 632 30 2 4225 4856 128991467 128992091 0.000000e+00 955
26 TraesCS4D01G195000 chr5B 86.992 123 16 0 2274 2396 634280200 634280078 6.550000e-29 139
27 TraesCS4D01G195000 chr5D 94.534 622 27 3 4236 4856 501410016 501410631 0.000000e+00 953
28 TraesCS4D01G195000 chr2A 83.654 208 32 2 2565 2771 40537828 40538034 1.380000e-45 195
29 TraesCS4D01G195000 chr2A 86.364 154 18 2 2277 2427 40537639 40537792 1.080000e-36 165
30 TraesCS4D01G195000 chr2A 81.818 187 28 4 1636 1816 40537377 40537563 8.420000e-33 152
31 TraesCS4D01G195000 chr2A 85.484 124 18 0 2895 3018 40538149 40538272 3.940000e-26 130
32 TraesCS4D01G195000 chr2B 83.173 208 33 2 2565 2771 62546945 62547151 6.420000e-44 189
33 TraesCS4D01G195000 chr2B 90.244 123 12 0 2274 2396 62546753 62546875 1.400000e-35 161
34 TraesCS4D01G195000 chr2B 86.614 127 17 0 1690 1816 62546540 62546666 1.820000e-29 141
35 TraesCS4D01G195000 chr2B 86.957 115 15 0 2905 3019 62547296 62547410 3.940000e-26 130
36 TraesCS4D01G195000 chr3A 83.582 201 27 5 2563 2760 598974869 598975066 2.990000e-42 183
37 TraesCS4D01G195000 chr3A 86.992 123 12 3 2269 2389 598974367 598974487 8.480000e-28 135
38 TraesCS4D01G195000 chr1A 92.562 121 9 0 2277 2397 236303428 236303308 1.800000e-39 174
39 TraesCS4D01G195000 chr1A 86.885 122 16 0 1695 1816 514434109 514433988 2.360000e-28 137
40 TraesCS4D01G195000 chr1A 86.885 122 16 0 1695 1816 514503395 514503274 2.360000e-28 137
41 TraesCS4D01G195000 chrUn 86.885 122 16 0 1695 1816 427445272 427445393 2.360000e-28 137


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 TraesCS4D01G195000 chr4D 338365523 338370378 4855 False 8968.00 8968 100.0000 1 4856 1 chr4D.!!$F2 4855
1 TraesCS4D01G195000 chr4D 37261136 37261763 627 True 948.00 948 93.8490 4224 4856 1 chr4D.!!$R1 632
2 TraesCS4D01G195000 chr4B 417349382 417353490 4108 False 1083.20 2887 94.3518 5 4099 5 chr4B.!!$F1 4094
3 TraesCS4D01G195000 chr4B 64814332 64814944 612 True 959.00 959 94.8220 4239 4856 1 chr4B.!!$R1 617
4 TraesCS4D01G195000 chr4A 133839942 133844335 4393 True 1356.25 2702 91.7960 4 4204 4 chr4A.!!$R1 4200
5 TraesCS4D01G195000 chr3D 156247830 156248444 614 False 970.00 970 95.0080 4236 4856 1 chr3D.!!$F1 620
6 TraesCS4D01G195000 chr3D 330685442 330686056 614 True 968.00 968 94.9920 4236 4854 1 chr3D.!!$R2 618
7 TraesCS4D01G195000 chr3D 90194830 90195443 613 True 957.00 957 94.6860 4236 4856 1 chr3D.!!$R1 620
8 TraesCS4D01G195000 chr3B 267006126 267006754 628 True 965.00 965 94.3130 4225 4856 1 chr3B.!!$R1 631
9 TraesCS4D01G195000 chr2D 424669562 424670186 624 False 961.00 961 94.3040 4225 4855 1 chr2D.!!$F1 630
10 TraesCS4D01G195000 chr5B 128991467 128992091 624 False 955.00 955 94.1460 4225 4856 1 chr5B.!!$F1 631
11 TraesCS4D01G195000 chr5D 501410016 501410631 615 False 953.00 953 94.5340 4236 4856 1 chr5D.!!$F1 620

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
261 265 0.248215 GCATCTCGCACCAAAATCCG 60.248 55.0 0.0 0.0 41.79 4.18 F
608 634 0.836400 GGGGAGTGTTGGTGGAGAGA 60.836 60.0 0.0 0.0 0.00 3.10 F
1890 1971 0.109532 TTGTGGGGTTGCGATCTGAA 59.890 50.0 0.0 0.0 0.00 3.02 F
2171 2324 0.031994 GGCACTGGCACAACGAAAAT 59.968 50.0 0.0 0.0 43.71 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 1908 0.160182 GCGTAAAACGGTCACACGAG 59.840 55.0 11.09 0.00 42.82 4.18 R
2077 2229 0.247695 GATGCTCAAACTAACGCGGC 60.248 55.0 12.47 0.29 0.00 6.53 R
2825 3145 0.182299 TGTGGTTGTCAGTGCCATGA 59.818 50.0 0.00 0.00 34.52 3.07 R
3899 4357 1.171308 ATCTGCATGCAACACTGACC 58.829 50.0 22.88 0.00 0.00 4.02 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
33 34 2.555757 CAGAAAGCACCAAGGAAGGAAG 59.444 50.000 0.00 0.00 0.00 3.46
117 121 3.753434 CGGCTGCCTCGTCTGAGT 61.753 66.667 17.92 0.00 40.85 3.41
118 122 2.183046 GGCTGCCTCGTCTGAGTC 59.817 66.667 12.43 0.00 40.85 3.36
119 123 2.202544 GCTGCCTCGTCTGAGTCG 60.203 66.667 0.00 0.00 40.85 4.18
121 125 1.135731 CTGCCTCGTCTGAGTCGTC 59.864 63.158 0.00 0.00 40.85 4.20
122 126 1.302383 CTGCCTCGTCTGAGTCGTCT 61.302 60.000 0.00 0.00 40.85 4.18
123 127 1.299562 TGCCTCGTCTGAGTCGTCTC 61.300 60.000 2.47 2.47 40.85 3.36
124 128 1.299562 GCCTCGTCTGAGTCGTCTCA 61.300 60.000 11.83 11.83 46.85 3.27
160 164 2.202743 TTGCTTCCCGATCTCGCG 60.203 61.111 0.00 0.00 38.18 5.87
164 168 3.486252 CTTCCCGATCTCGCGACCC 62.486 68.421 3.71 0.00 38.18 4.46
185 189 3.753434 CCAGGCGAGCGAGACAGT 61.753 66.667 0.00 0.00 0.00 3.55
219 223 2.612212 ACTCCATGTCACAAACGAACAC 59.388 45.455 0.00 0.00 0.00 3.32
261 265 0.248215 GCATCTCGCACCAAAATCCG 60.248 55.000 0.00 0.00 41.79 4.18
274 278 3.799420 CCAAAATCCGAAAACGAAAAGCA 59.201 39.130 0.00 0.00 0.00 3.91
305 309 6.264067 AGAGGAATATCAATTAGCAAGCAACC 59.736 38.462 0.00 0.00 0.00 3.77
361 365 1.165270 ACAAGGCAAGTAACGGATGC 58.835 50.000 0.00 0.00 39.33 3.91
405 411 6.042093 TGCCAATGTAACCTCCAAATTAAACA 59.958 34.615 0.00 0.00 0.00 2.83
406 412 7.102993 GCCAATGTAACCTCCAAATTAAACAT 58.897 34.615 0.00 0.00 0.00 2.71
572 598 9.084533 CCTACCAAATATATATAGAGAGGGAGC 57.915 40.741 0.00 0.00 0.00 4.70
608 634 0.836400 GGGGAGTGTTGGTGGAGAGA 60.836 60.000 0.00 0.00 0.00 3.10
678 710 1.494960 ACCAAAGGGAAGCAAGCAAA 58.505 45.000 0.00 0.00 38.05 3.68
681 713 1.688197 CAAAGGGAAGCAAGCAAAGGA 59.312 47.619 0.00 0.00 0.00 3.36
682 714 2.086610 AAGGGAAGCAAGCAAAGGAA 57.913 45.000 0.00 0.00 0.00 3.36
686 718 2.599659 GGAAGCAAGCAAAGGAAATCG 58.400 47.619 0.00 0.00 0.00 3.34
820 871 2.813754 CAGCTCTCCATTTTCCGTTTCA 59.186 45.455 0.00 0.00 0.00 2.69
822 873 4.635765 CAGCTCTCCATTTTCCGTTTCATA 59.364 41.667 0.00 0.00 0.00 2.15
860 911 2.448961 AGGGAGAGAGCTAGATAGGCAA 59.551 50.000 0.00 0.00 0.00 4.52
864 918 4.097892 GGAGAGAGCTAGATAGGCAATAGC 59.902 50.000 0.00 0.00 41.79 2.97
1194 1265 4.083862 GACTTCCCCTTCGGCGCT 62.084 66.667 7.64 0.00 0.00 5.92
1412 1486 4.218686 GGTGGTGGTGGCCAAGGT 62.219 66.667 7.24 0.00 40.68 3.50
1710 1784 1.007336 CGGTGTACAAGGAGACGCAC 61.007 60.000 0.00 0.00 0.00 5.34
1890 1971 0.109532 TTGTGGGGTTGCGATCTGAA 59.890 50.000 0.00 0.00 0.00 3.02
1965 2046 0.952280 GTACGAGCCGGAGATCATCA 59.048 55.000 5.05 0.00 0.00 3.07
1973 2054 2.408050 CCGGAGATCATCATCGGTTTC 58.592 52.381 0.00 0.00 36.38 2.78
2055 2151 2.037251 TGAGACAAACACCACTAGGAGC 59.963 50.000 0.00 0.00 38.69 4.70
2056 2152 2.037251 GAGACAAACACCACTAGGAGCA 59.963 50.000 0.00 0.00 38.69 4.26
2057 2153 2.037772 AGACAAACACCACTAGGAGCAG 59.962 50.000 0.00 0.00 38.69 4.24
2076 2228 4.833380 AGCAGTGTTCTCTACTCCTGTTAA 59.167 41.667 0.00 0.00 32.45 2.01
2077 2229 5.047660 AGCAGTGTTCTCTACTCCTGTTAAG 60.048 44.000 0.00 0.00 32.45 1.85
2085 2237 0.604578 ACTCCTGTTAAGCCGCGTTA 59.395 50.000 4.92 0.00 0.00 3.18
2160 2313 3.368571 GAGGCAAGTGGCACTGGC 61.369 66.667 34.11 34.11 44.44 4.85
2161 2314 4.208403 AGGCAAGTGGCACTGGCA 62.208 61.111 39.53 0.07 46.98 4.92
2169 2322 1.750780 TGGCACTGGCACAACGAAA 60.751 52.632 0.07 0.00 43.71 3.46
2170 2323 1.315981 TGGCACTGGCACAACGAAAA 61.316 50.000 0.07 0.00 43.71 2.29
2171 2324 0.031994 GGCACTGGCACAACGAAAAT 59.968 50.000 0.00 0.00 43.71 1.82
2172 2325 1.130955 GCACTGGCACAACGAAAATG 58.869 50.000 0.00 0.00 38.70 2.32
2173 2326 1.268999 GCACTGGCACAACGAAAATGA 60.269 47.619 0.00 0.00 38.70 2.57
2175 2328 2.981805 CACTGGCACAACGAAAATGATG 59.018 45.455 0.00 0.00 38.70 3.07
2176 2329 1.987770 CTGGCACAACGAAAATGATGC 59.012 47.619 0.00 0.00 38.70 3.91
2178 2331 1.720852 GGCACAACGAAAATGATGCAC 59.279 47.619 0.00 0.00 34.73 4.57
2179 2332 2.392821 GCACAACGAAAATGATGCACA 58.607 42.857 0.00 0.00 33.27 4.57
2180 2333 2.793790 GCACAACGAAAATGATGCACAA 59.206 40.909 0.00 0.00 33.27 3.33
2182 2335 3.042189 ACAACGAAAATGATGCACAACG 58.958 40.909 0.00 0.00 0.00 4.10
2184 2337 4.215201 CAACGAAAATGATGCACAACGTA 58.785 39.130 0.00 0.00 32.20 3.57
2185 2338 3.805823 ACGAAAATGATGCACAACGTAC 58.194 40.909 0.00 0.00 0.00 3.67
2186 2339 3.496884 ACGAAAATGATGCACAACGTACT 59.503 39.130 0.00 0.00 0.00 2.73
2187 2340 3.840209 CGAAAATGATGCACAACGTACTG 59.160 43.478 0.00 0.00 0.00 2.74
2188 2341 4.610456 CGAAAATGATGCACAACGTACTGT 60.610 41.667 0.00 0.00 0.00 3.55
2189 2342 5.388994 CGAAAATGATGCACAACGTACTGTA 60.389 40.000 0.00 0.00 0.00 2.74
2191 2344 2.333926 TGATGCACAACGTACTGTAGC 58.666 47.619 0.00 0.00 0.00 3.58
2192 2345 2.288518 TGATGCACAACGTACTGTAGCA 60.289 45.455 15.08 15.08 37.57 3.49
2193 2346 2.448926 TGCACAACGTACTGTAGCAT 57.551 45.000 11.10 0.00 32.29 3.79
2195 2348 2.478514 TGCACAACGTACTGTAGCATTG 59.521 45.455 11.10 0.00 32.29 2.82
2197 2350 3.059188 GCACAACGTACTGTAGCATTGTT 60.059 43.478 7.98 0.00 0.00 2.83
2198 2351 4.454231 CACAACGTACTGTAGCATTGTTG 58.546 43.478 7.98 10.04 40.61 3.33
2199 2352 3.496884 ACAACGTACTGTAGCATTGTTGG 59.503 43.478 15.15 0.00 39.48 3.77
2201 2354 3.064207 ACGTACTGTAGCATTGTTGGTG 58.936 45.455 0.00 0.00 34.79 4.17
2202 2355 3.064207 CGTACTGTAGCATTGTTGGTGT 58.936 45.455 0.00 0.00 34.79 4.16
2203 2356 3.122948 CGTACTGTAGCATTGTTGGTGTC 59.877 47.826 0.00 0.00 34.79 3.67
2205 2358 3.141398 ACTGTAGCATTGTTGGTGTCTG 58.859 45.455 0.00 0.00 34.79 3.51
2206 2359 2.485426 CTGTAGCATTGTTGGTGTCTGG 59.515 50.000 0.00 0.00 34.79 3.86
2209 2362 0.318955 GCATTGTTGGTGTCTGGCAC 60.319 55.000 3.25 3.25 46.97 5.01
2228 2508 5.242615 TGGCACAATGCTGTATTAGTTTGAA 59.757 36.000 0.13 0.00 44.28 2.69
2230 2510 5.287035 GCACAATGCTGTATTAGTTTGAAGC 59.713 40.000 0.00 0.00 40.96 3.86
2479 2759 2.224606 CGTACGTGCCTAATCCCTCTA 58.775 52.381 7.22 0.00 0.00 2.43
2480 2760 2.620115 CGTACGTGCCTAATCCCTCTAA 59.380 50.000 7.22 0.00 0.00 2.10
2481 2761 3.255149 CGTACGTGCCTAATCCCTCTAAT 59.745 47.826 7.22 0.00 0.00 1.73
2482 2762 4.261909 CGTACGTGCCTAATCCCTCTAATT 60.262 45.833 7.22 0.00 0.00 1.40
2483 2763 4.073293 ACGTGCCTAATCCCTCTAATTG 57.927 45.455 0.00 0.00 0.00 2.32
2484 2764 3.454812 ACGTGCCTAATCCCTCTAATTGT 59.545 43.478 0.00 0.00 0.00 2.71
2487 2767 3.459598 TGCCTAATCCCTCTAATTGTGCT 59.540 43.478 0.00 0.00 0.00 4.40
2488 2768 3.817647 GCCTAATCCCTCTAATTGTGCTG 59.182 47.826 0.00 0.00 0.00 4.41
2490 2770 5.440610 CCTAATCCCTCTAATTGTGCTGTT 58.559 41.667 0.00 0.00 0.00 3.16
2493 2773 7.721399 CCTAATCCCTCTAATTGTGCTGTTATT 59.279 37.037 0.00 0.00 0.00 1.40
2494 2774 9.778741 CTAATCCCTCTAATTGTGCTGTTATTA 57.221 33.333 0.00 0.00 0.00 0.98
2496 2776 6.046593 TCCCTCTAATTGTGCTGTTATTACG 58.953 40.000 0.00 0.00 0.00 3.18
2497 2777 5.815740 CCCTCTAATTGTGCTGTTATTACGT 59.184 40.000 0.00 0.00 0.00 3.57
2512 2803 6.017026 TGTTATTACGTGATCTAGCCTGAGAG 60.017 42.308 0.00 0.00 0.00 3.20
2527 2818 1.287442 TGAGAGAGAGGAGCTCATGGT 59.713 52.381 17.19 0.00 46.45 3.55
2542 2833 2.158579 TCATGGTCATGGATGGATGGTG 60.159 50.000 10.61 0.00 39.24 4.17
2544 2835 2.137702 TGGTCATGGATGGATGGTGAT 58.862 47.619 0.00 0.00 0.00 3.06
2546 2837 2.511659 GTCATGGATGGATGGTGATGG 58.488 52.381 0.00 0.00 0.00 3.51
2556 2847 0.033894 ATGGTGATGGTGCATGCTGA 60.034 50.000 20.33 2.57 0.00 4.26
2700 2991 1.227823 CACGCCAAGAACTGGGTCA 60.228 57.895 0.00 0.00 46.54 4.02
2774 3092 5.107453 CGACATGAAAGTCCTGTAAGTTGTC 60.107 44.000 0.00 0.00 35.07 3.18
2775 3093 5.063880 ACATGAAAGTCCTGTAAGTTGTCC 58.936 41.667 0.00 0.00 0.00 4.02
2776 3094 4.764050 TGAAAGTCCTGTAAGTTGTCCA 57.236 40.909 0.00 0.00 0.00 4.02
2777 3095 5.304686 TGAAAGTCCTGTAAGTTGTCCAT 57.695 39.130 0.00 0.00 0.00 3.41
2778 3096 5.063204 TGAAAGTCCTGTAAGTTGTCCATG 58.937 41.667 0.00 0.00 0.00 3.66
2779 3097 3.703001 AGTCCTGTAAGTTGTCCATGG 57.297 47.619 4.97 4.97 0.00 3.66
2781 3099 3.008049 AGTCCTGTAAGTTGTCCATGGAC 59.992 47.826 33.97 33.97 44.77 4.02
2791 3109 2.472695 GTCCATGGACAGTAGCAACA 57.527 50.000 35.21 0.00 44.02 3.33
2792 3110 2.991250 GTCCATGGACAGTAGCAACAT 58.009 47.619 35.21 0.00 44.02 2.71
2793 3111 3.347216 GTCCATGGACAGTAGCAACATT 58.653 45.455 35.21 0.00 44.02 2.71
2819 3139 2.029290 AGTTGCTTTGGTATCTCGACGT 60.029 45.455 0.00 0.00 0.00 4.34
2820 3140 3.192001 AGTTGCTTTGGTATCTCGACGTA 59.808 43.478 0.00 0.00 0.00 3.57
2821 3141 3.141002 TGCTTTGGTATCTCGACGTAC 57.859 47.619 0.00 0.00 0.00 3.67
2822 3142 2.751259 TGCTTTGGTATCTCGACGTACT 59.249 45.455 0.00 0.00 0.00 2.73
2823 3143 3.940852 TGCTTTGGTATCTCGACGTACTA 59.059 43.478 0.00 0.00 0.00 1.82
2824 3144 4.201851 TGCTTTGGTATCTCGACGTACTAC 60.202 45.833 0.00 0.00 0.00 2.73
2825 3145 4.034975 GCTTTGGTATCTCGACGTACTACT 59.965 45.833 0.00 0.00 0.00 2.57
2826 3146 5.725110 TTTGGTATCTCGACGTACTACTC 57.275 43.478 0.00 0.00 0.00 2.59
2827 3147 4.391405 TGGTATCTCGACGTACTACTCA 57.609 45.455 0.00 0.00 0.00 3.41
2828 3148 4.953667 TGGTATCTCGACGTACTACTCAT 58.046 43.478 0.00 0.00 0.00 2.90
2829 3149 4.748600 TGGTATCTCGACGTACTACTCATG 59.251 45.833 0.00 0.00 0.00 3.07
2832 3152 1.669265 CTCGACGTACTACTCATGGCA 59.331 52.381 0.00 0.00 0.00 4.92
2835 3155 2.791503 CGACGTACTACTCATGGCACTG 60.792 54.545 0.00 0.00 0.00 3.66
2836 3156 2.422479 GACGTACTACTCATGGCACTGA 59.578 50.000 0.00 0.00 0.00 3.41
2838 3158 2.163613 CGTACTACTCATGGCACTGACA 59.836 50.000 0.00 0.00 0.00 3.58
2841 3161 2.289694 ACTACTCATGGCACTGACAACC 60.290 50.000 0.00 0.00 0.00 3.77
2842 3162 0.473755 ACTCATGGCACTGACAACCA 59.526 50.000 0.00 0.00 37.99 3.67
2843 3163 0.877071 CTCATGGCACTGACAACCAC 59.123 55.000 0.00 0.00 35.99 4.16
2844 3164 0.182299 TCATGGCACTGACAACCACA 59.818 50.000 0.00 0.00 35.99 4.17
2845 3165 1.202915 TCATGGCACTGACAACCACAT 60.203 47.619 0.00 0.00 35.99 3.21
2846 3166 2.039613 TCATGGCACTGACAACCACATA 59.960 45.455 0.00 0.00 35.99 2.29
2847 3167 1.890876 TGGCACTGACAACCACATAC 58.109 50.000 0.00 0.00 0.00 2.39
2849 3169 0.796312 GCACTGACAACCACATACGG 59.204 55.000 0.00 0.00 0.00 4.02
2850 3170 1.606994 GCACTGACAACCACATACGGA 60.607 52.381 0.00 0.00 0.00 4.69
2852 3172 3.677700 GCACTGACAACCACATACGGATA 60.678 47.826 0.00 0.00 0.00 2.59
3045 3397 6.813649 TCACGTAAGCCCTACTATACTATACG 59.186 42.308 0.00 0.00 45.62 3.06
3046 3398 6.591834 CACGTAAGCCCTACTATACTATACGT 59.408 42.308 0.00 0.00 45.09 3.57
3047 3399 7.759886 CACGTAAGCCCTACTATACTATACGTA 59.240 40.741 0.00 0.00 43.17 3.57
3120 3492 5.409643 TTGCTTCAGTTTTTCTTCTCTCG 57.590 39.130 0.00 0.00 0.00 4.04
3150 3522 7.105241 AGTTTCTTTGCTTCAGTTCAGATTT 57.895 32.000 0.00 0.00 0.00 2.17
3179 3551 4.544762 CGTGTGCAGTGTACGCTA 57.455 55.556 20.38 0.00 0.00 4.26
3185 3557 1.862201 GTGCAGTGTACGCTACAAACA 59.138 47.619 10.90 1.71 40.93 2.83
3250 3622 2.959071 GCGCGCAGTGAGATCTCC 60.959 66.667 29.10 11.17 43.07 3.71
3270 3648 4.079253 TCCCTTTCAATTAGGTGTTGAGC 58.921 43.478 0.00 0.00 36.96 4.26
3395 3787 0.686769 GGCGAGAGAGGACCCCTAAA 60.687 60.000 0.00 0.00 31.76 1.85
3624 4078 2.853914 GTGCTCAAGACGTTCCGC 59.146 61.111 0.00 0.00 0.00 5.54
3831 4285 4.148825 GCCCGCATCGTCTCCAGT 62.149 66.667 0.00 0.00 0.00 4.00
3845 4299 2.669569 CAGTGCCTCCACCCAACG 60.670 66.667 0.00 0.00 43.09 4.10
3850 4304 2.672996 CCTCCACCCAACGCCAAG 60.673 66.667 0.00 0.00 0.00 3.61
3899 4357 3.068691 TCCAACGAGGCTCCTCCG 61.069 66.667 9.32 0.00 39.77 4.63
3902 4360 3.069318 AACGAGGCTCCTCCGGTC 61.069 66.667 9.32 0.00 39.77 4.79
3912 4370 1.003355 CCTCCGGTCAGTGTTGCAT 60.003 57.895 0.00 0.00 0.00 3.96
3913 4371 1.300971 CCTCCGGTCAGTGTTGCATG 61.301 60.000 0.00 0.00 0.00 4.06
3914 4372 1.915614 CTCCGGTCAGTGTTGCATGC 61.916 60.000 11.82 11.82 0.00 4.06
3915 4373 2.260154 CCGGTCAGTGTTGCATGCA 61.260 57.895 18.46 18.46 0.00 3.96
3916 4374 1.208358 CGGTCAGTGTTGCATGCAG 59.792 57.895 21.50 9.09 0.00 4.41
3917 4375 1.229975 CGGTCAGTGTTGCATGCAGA 61.230 55.000 21.50 11.53 0.00 4.26
3934 4397 5.193663 TGCAGATACAGATACAGAAGAGC 57.806 43.478 0.00 0.00 0.00 4.09
3982 4445 1.005156 GATGCCCGCCATCTCTCTC 60.005 63.158 6.95 0.00 45.58 3.20
3993 4457 4.074970 GCCATCTCTCTCTTTTTCACCAA 58.925 43.478 0.00 0.00 0.00 3.67
4026 4490 1.423845 CGTAAAGCCGTCATGTGCC 59.576 57.895 0.00 0.00 0.00 5.01
4115 4581 3.319122 GTGTTTGACTGGCTCATTTTCCT 59.681 43.478 0.00 0.00 0.00 3.36
4123 4589 1.340405 GGCTCATTTTCCTCTCCTGCA 60.340 52.381 0.00 0.00 0.00 4.41
4197 4663 0.615331 GTGCTCTGGTGATCAAGGGA 59.385 55.000 0.00 0.00 0.00 4.20
4204 4670 5.337169 GCTCTGGTGATCAAGGGAGATATAC 60.337 48.000 18.30 3.21 0.00 1.47
4205 4671 5.715921 TCTGGTGATCAAGGGAGATATACA 58.284 41.667 0.00 0.00 0.00 2.29
4206 4672 5.540337 TCTGGTGATCAAGGGAGATATACAC 59.460 44.000 0.00 0.00 0.00 2.90
4207 4673 5.467738 TGGTGATCAAGGGAGATATACACT 58.532 41.667 0.00 0.00 0.00 3.55
4208 4674 5.540337 TGGTGATCAAGGGAGATATACACTC 59.460 44.000 0.00 0.00 0.00 3.51
4209 4675 5.777732 GGTGATCAAGGGAGATATACACTCT 59.222 44.000 0.00 0.00 35.10 3.24
4210 4676 6.268847 GGTGATCAAGGGAGATATACACTCTT 59.731 42.308 0.00 0.00 35.10 2.85
4211 4677 7.375053 GTGATCAAGGGAGATATACACTCTTC 58.625 42.308 0.00 0.00 35.10 2.87
4212 4678 7.014711 GTGATCAAGGGAGATATACACTCTTCA 59.985 40.741 0.00 0.00 35.10 3.02
4213 4679 6.716934 TCAAGGGAGATATACACTCTTCAC 57.283 41.667 8.15 0.00 35.10 3.18
4214 4680 5.299531 TCAAGGGAGATATACACTCTTCACG 59.700 44.000 8.15 0.00 35.10 4.35
4215 4681 3.570550 AGGGAGATATACACTCTTCACGC 59.429 47.826 8.15 0.00 35.10 5.34
4216 4682 3.318275 GGGAGATATACACTCTTCACGCA 59.682 47.826 8.15 0.00 35.10 5.24
4217 4683 4.021894 GGGAGATATACACTCTTCACGCAT 60.022 45.833 8.15 0.00 35.10 4.73
4218 4684 4.920340 GGAGATATACACTCTTCACGCATG 59.080 45.833 8.15 0.00 35.10 4.06
4219 4685 4.302455 AGATATACACTCTTCACGCATGC 58.698 43.478 7.91 7.91 0.00 4.06
4220 4686 2.680312 ATACACTCTTCACGCATGCT 57.320 45.000 17.13 0.00 0.00 3.79
4221 4687 3.801114 ATACACTCTTCACGCATGCTA 57.199 42.857 17.13 0.00 0.00 3.49
4222 4688 1.714794 ACACTCTTCACGCATGCTAC 58.285 50.000 17.13 0.00 0.00 3.58
4233 4699 1.528586 CGCATGCTACCTGTAAGATGC 59.471 52.381 17.13 0.00 34.07 3.91
4318 4784 2.941064 CACGGACCTCGACTATACAAGA 59.059 50.000 0.00 0.00 42.43 3.02
4342 4810 2.515901 GAGGCGGGCCCAATACAT 59.484 61.111 24.92 5.09 36.58 2.29
4442 4912 1.610624 GGAACTCCTCAAATGACGCCA 60.611 52.381 0.00 0.00 0.00 5.69
4484 4954 9.473007 TCATGATATCTACAAATTGTTGGGAAA 57.527 29.630 3.17 0.00 39.22 3.13
4587 5057 0.179084 CGATGATGCACCGGGTTAGT 60.179 55.000 6.32 0.00 0.00 2.24
4614 5084 1.518056 TAGACCGCCGAGACGTTGTT 61.518 55.000 0.00 0.00 0.00 2.83
4663 5133 1.546548 GGGCAAGAAAGCTCCTGAAGT 60.547 52.381 0.00 0.00 34.17 3.01
4819 5289 2.104859 CGAGGTGGAGCGACGAGTA 61.105 63.158 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.840635 GTGCTTTCTGACCTATCCCCT 59.159 52.381 0.00 0.00 0.00 4.79
3 4 1.559682 TGGTGCTTTCTGACCTATCCC 59.440 52.381 0.00 0.00 32.98 3.85
4 5 3.274288 CTTGGTGCTTTCTGACCTATCC 58.726 50.000 0.00 0.00 32.98 2.59
5 6 3.055094 TCCTTGGTGCTTTCTGACCTATC 60.055 47.826 0.00 0.00 32.98 2.08
6 7 2.912956 TCCTTGGTGCTTTCTGACCTAT 59.087 45.455 0.00 0.00 32.98 2.57
7 8 2.334977 TCCTTGGTGCTTTCTGACCTA 58.665 47.619 0.00 0.00 32.98 3.08
8 9 1.140312 TCCTTGGTGCTTTCTGACCT 58.860 50.000 0.00 0.00 32.98 3.85
33 34 2.143122 TCGTGTTCTTGCACAAGATCC 58.857 47.619 13.54 8.37 45.78 3.36
52 53 2.029365 GCTTCGTCGCTACTCCATTTTC 59.971 50.000 0.00 0.00 0.00 2.29
119 123 3.537297 GCGAGCGAGCGTTGAGAC 61.537 66.667 0.00 0.00 0.00 3.36
122 126 3.932580 AATGGCGAGCGAGCGTTGA 62.933 57.895 0.00 0.00 38.18 3.18
123 127 3.490759 AATGGCGAGCGAGCGTTG 61.491 61.111 0.00 0.00 38.18 4.10
124 128 3.490759 CAATGGCGAGCGAGCGTT 61.491 61.111 0.00 0.00 38.18 4.84
185 189 3.239449 ACATGGAGTGGTTAGACTGTGA 58.761 45.455 0.00 0.00 0.00 3.58
219 223 0.389296 TGGTTGTATGGTCGCGAGTG 60.389 55.000 10.24 0.00 0.00 3.51
252 256 3.799420 TGCTTTTCGTTTTCGGATTTTGG 59.201 39.130 0.00 0.00 44.25 3.28
253 257 4.266502 TGTGCTTTTCGTTTTCGGATTTTG 59.733 37.500 0.00 0.00 44.25 2.44
254 258 4.425520 TGTGCTTTTCGTTTTCGGATTTT 58.574 34.783 0.00 0.00 44.25 1.82
255 259 4.035278 TGTGCTTTTCGTTTTCGGATTT 57.965 36.364 0.00 0.00 44.25 2.17
256 260 3.701532 TGTGCTTTTCGTTTTCGGATT 57.298 38.095 0.00 0.00 44.25 3.01
257 261 3.701532 TTGTGCTTTTCGTTTTCGGAT 57.298 38.095 0.00 0.00 44.25 4.18
258 262 3.489180 TTTGTGCTTTTCGTTTTCGGA 57.511 38.095 0.00 0.00 44.25 4.55
261 265 5.575218 TCCTCTTTTTGTGCTTTTCGTTTTC 59.425 36.000 0.00 0.00 0.00 2.29
305 309 7.540745 GCGTATTTTGGGGTAGCATATTTAATG 59.459 37.037 0.00 0.00 0.00 1.90
361 365 2.610374 GCATTGCCTTGCCAAACATATG 59.390 45.455 0.00 0.00 36.60 1.78
514 530 7.693969 TCTCTTCAATTTCCTCCATTCTTTC 57.306 36.000 0.00 0.00 0.00 2.62
568 594 2.559231 CCTCCTCCTAATTACTCGCTCC 59.441 54.545 0.00 0.00 0.00 4.70
571 597 1.619332 CCCCTCCTCCTAATTACTCGC 59.381 57.143 0.00 0.00 0.00 5.03
572 598 2.158355 TCCCCCTCCTCCTAATTACTCG 60.158 54.545 0.00 0.00 0.00 4.18
608 634 5.253330 TCTTTTATTGTTGCGGGATCTCTT 58.747 37.500 0.00 0.00 0.00 2.85
678 710 2.649531 TGTTGGGTGTTCGATTTCCT 57.350 45.000 0.00 0.00 0.00 3.36
681 713 2.364002 CCCTTTGTTGGGTGTTCGATTT 59.636 45.455 0.00 0.00 42.25 2.17
682 714 1.960689 CCCTTTGTTGGGTGTTCGATT 59.039 47.619 0.00 0.00 42.25 3.34
686 718 1.328279 CTCCCCTTTGTTGGGTGTTC 58.672 55.000 0.00 0.00 45.70 3.18
822 873 8.272659 TCTCTCCCTCTATGAAATGAAATGAT 57.727 34.615 0.00 0.00 0.00 2.45
941 1003 1.829222 GAACTTACCACGATCTCCCCA 59.171 52.381 0.00 0.00 0.00 4.96
1640 1714 2.960170 GGTACAGGTCGCACGTCT 59.040 61.111 0.00 0.00 0.00 4.18
1710 1784 2.962569 TCCGTCAGGAACTCGCAG 59.037 61.111 0.00 0.00 45.12 5.18
1824 1898 2.052157 GGTCACACGAGAACGAAGAAG 58.948 52.381 0.00 0.00 42.66 2.85
1833 1907 1.757574 CGTAAAACGGTCACACGAGA 58.242 50.000 0.00 0.00 38.08 4.04
1834 1908 0.160182 GCGTAAAACGGTCACACGAG 59.840 55.000 11.09 0.00 42.82 4.18
1919 2000 1.674322 AAACCAGACCGGCCATTCG 60.674 57.895 0.00 0.00 39.03 3.34
1973 2054 1.073199 AAGTGGCCTCAGTTTCCGG 59.927 57.895 3.32 0.00 33.01 5.14
1983 2064 4.104261 AGGAGTAGTAAAAACAAGTGGCCT 59.896 41.667 3.32 0.00 0.00 5.19
2022 2103 7.967303 GTGGTGTTTGTCTCATAGTACTAGTAC 59.033 40.741 23.03 23.03 36.35 2.73
2026 2107 7.338703 CCTAGTGGTGTTTGTCTCATAGTACTA 59.661 40.741 4.77 4.77 0.00 1.82
2028 2109 6.152323 TCCTAGTGGTGTTTGTCTCATAGTAC 59.848 42.308 0.00 0.00 34.23 2.73
2030 2111 5.084519 TCCTAGTGGTGTTTGTCTCATAGT 58.915 41.667 0.00 0.00 34.23 2.12
2031 2112 5.655488 CTCCTAGTGGTGTTTGTCTCATAG 58.345 45.833 0.00 0.00 34.23 2.23
2055 2151 5.164954 GCTTAACAGGAGTAGAGAACACTG 58.835 45.833 0.00 0.00 39.73 3.66
2056 2152 4.221041 GGCTTAACAGGAGTAGAGAACACT 59.779 45.833 0.00 0.00 0.00 3.55
2057 2153 4.496360 GGCTTAACAGGAGTAGAGAACAC 58.504 47.826 0.00 0.00 0.00 3.32
2076 2228 0.673644 ATGCTCAAACTAACGCGGCT 60.674 50.000 12.47 0.00 0.00 5.52
2077 2229 0.247695 GATGCTCAAACTAACGCGGC 60.248 55.000 12.47 0.29 0.00 6.53
2085 2237 0.322975 AGCTGTCGGATGCTCAAACT 59.677 50.000 3.21 0.00 33.90 2.66
2117 2270 0.382873 GCCGAAAAACAGTTTCCCGT 59.617 50.000 14.87 0.00 0.00 5.28
2144 2297 4.208403 TGCCAGTGCCACTTGCCT 62.208 61.111 17.26 0.00 36.17 4.75
2145 2298 3.982241 GTGCCAGTGCCACTTGCC 61.982 66.667 17.26 6.12 36.17 4.52
2156 2309 1.987770 GCATCATTTTCGTTGTGCCAG 59.012 47.619 0.00 0.00 0.00 4.85
2157 2310 1.339291 TGCATCATTTTCGTTGTGCCA 59.661 42.857 0.00 0.00 0.00 4.92
2158 2311 1.720852 GTGCATCATTTTCGTTGTGCC 59.279 47.619 0.00 0.00 0.00 5.01
2159 2312 2.392821 TGTGCATCATTTTCGTTGTGC 58.607 42.857 0.00 0.00 0.00 4.57
2160 2313 3.121729 CGTTGTGCATCATTTTCGTTGTG 60.122 43.478 0.00 0.00 0.00 3.33
2161 2314 3.042189 CGTTGTGCATCATTTTCGTTGT 58.958 40.909 0.00 0.00 0.00 3.32
2162 2315 3.042189 ACGTTGTGCATCATTTTCGTTG 58.958 40.909 0.00 0.00 0.00 4.10
2164 2317 3.496884 AGTACGTTGTGCATCATTTTCGT 59.503 39.130 0.00 0.00 0.00 3.85
2165 2318 3.840209 CAGTACGTTGTGCATCATTTTCG 59.160 43.478 0.00 0.00 0.00 3.46
2167 2320 4.829064 ACAGTACGTTGTGCATCATTTT 57.171 36.364 0.00 0.00 0.00 1.82
2169 2322 3.370978 GCTACAGTACGTTGTGCATCATT 59.629 43.478 3.12 0.00 32.56 2.57
2170 2323 2.930040 GCTACAGTACGTTGTGCATCAT 59.070 45.455 3.12 0.00 32.56 2.45
2171 2324 2.288518 TGCTACAGTACGTTGTGCATCA 60.289 45.455 3.12 0.00 33.42 3.07
2172 2325 2.333926 TGCTACAGTACGTTGTGCATC 58.666 47.619 3.12 0.00 33.42 3.91
2173 2326 2.448926 TGCTACAGTACGTTGTGCAT 57.551 45.000 3.12 0.00 33.42 3.96
2175 2328 2.478894 ACAATGCTACAGTACGTTGTGC 59.521 45.455 14.76 5.71 42.77 4.57
2176 2329 4.454231 CAACAATGCTACAGTACGTTGTG 58.546 43.478 15.62 0.00 43.40 3.33
2178 2331 3.496884 ACCAACAATGCTACAGTACGTTG 59.503 43.478 0.00 10.92 38.48 4.10
2179 2332 3.496884 CACCAACAATGCTACAGTACGTT 59.503 43.478 0.00 0.00 0.00 3.99
2180 2333 3.064207 CACCAACAATGCTACAGTACGT 58.936 45.455 0.00 0.00 0.00 3.57
2182 2335 4.152402 CAGACACCAACAATGCTACAGTAC 59.848 45.833 0.00 0.00 0.00 2.73
2184 2337 3.141398 CAGACACCAACAATGCTACAGT 58.859 45.455 0.00 0.00 0.00 3.55
2185 2338 2.485426 CCAGACACCAACAATGCTACAG 59.515 50.000 0.00 0.00 0.00 2.74
2186 2339 2.503331 CCAGACACCAACAATGCTACA 58.497 47.619 0.00 0.00 0.00 2.74
2187 2340 1.200020 GCCAGACACCAACAATGCTAC 59.800 52.381 0.00 0.00 0.00 3.58
2188 2341 1.202867 TGCCAGACACCAACAATGCTA 60.203 47.619 0.00 0.00 0.00 3.49
2189 2342 0.467844 TGCCAGACACCAACAATGCT 60.468 50.000 0.00 0.00 0.00 3.79
2191 2344 3.871775 GTGCCAGACACCAACAATG 57.128 52.632 0.00 0.00 44.02 2.82
2199 2352 1.522668 TACAGCATTGTGCCAGACAC 58.477 50.000 0.00 0.00 46.52 3.67
2201 2354 3.941483 ACTAATACAGCATTGTGCCAGAC 59.059 43.478 0.00 0.00 46.52 3.51
2202 2355 4.220693 ACTAATACAGCATTGTGCCAGA 57.779 40.909 0.00 0.00 46.52 3.86
2203 2356 4.970662 AACTAATACAGCATTGTGCCAG 57.029 40.909 0.00 0.00 46.52 4.85
2205 2358 5.309323 TCAAACTAATACAGCATTGTGCC 57.691 39.130 0.00 0.00 46.52 5.01
2206 2359 5.287035 GCTTCAAACTAATACAGCATTGTGC 59.713 40.000 0.00 0.00 45.46 4.57
2209 2362 6.615088 AGTGCTTCAAACTAATACAGCATTG 58.385 36.000 0.00 0.00 39.36 2.82
2210 2363 6.824305 AGTGCTTCAAACTAATACAGCATT 57.176 33.333 0.00 0.00 39.36 3.56
2211 2364 6.540189 CCTAGTGCTTCAAACTAATACAGCAT 59.460 38.462 0.00 0.00 39.36 3.79
2212 2365 5.874810 CCTAGTGCTTCAAACTAATACAGCA 59.125 40.000 0.00 0.00 34.92 4.41
2213 2366 5.294552 CCCTAGTGCTTCAAACTAATACAGC 59.705 44.000 0.00 0.00 29.96 4.40
2214 2367 6.640518 TCCCTAGTGCTTCAAACTAATACAG 58.359 40.000 0.00 0.00 29.96 2.74
2228 2508 2.378634 GCCCCACATCCCTAGTGCT 61.379 63.158 0.00 0.00 35.69 4.40
2230 2510 0.982852 TCAGCCCCACATCCCTAGTG 60.983 60.000 0.00 0.00 36.76 2.74
2479 2759 6.985188 AGATCACGTAATAACAGCACAATT 57.015 33.333 0.00 0.00 0.00 2.32
2480 2760 6.201044 GCTAGATCACGTAATAACAGCACAAT 59.799 38.462 0.00 0.00 0.00 2.71
2481 2761 5.518847 GCTAGATCACGTAATAACAGCACAA 59.481 40.000 0.00 0.00 0.00 3.33
2482 2762 5.041287 GCTAGATCACGTAATAACAGCACA 58.959 41.667 0.00 0.00 0.00 4.57
2483 2763 4.444720 GGCTAGATCACGTAATAACAGCAC 59.555 45.833 0.00 0.00 0.00 4.40
2484 2764 4.341235 AGGCTAGATCACGTAATAACAGCA 59.659 41.667 0.00 0.00 0.00 4.41
2487 2767 5.826208 TCTCAGGCTAGATCACGTAATAACA 59.174 40.000 0.00 0.00 0.00 2.41
2488 2768 6.205076 TCTCTCAGGCTAGATCACGTAATAAC 59.795 42.308 0.00 0.00 0.00 1.89
2490 2770 5.866207 TCTCTCAGGCTAGATCACGTAATA 58.134 41.667 0.00 0.00 0.00 0.98
2493 2773 3.388350 TCTCTCTCAGGCTAGATCACGTA 59.612 47.826 0.00 0.00 0.00 3.57
2494 2774 2.171659 TCTCTCTCAGGCTAGATCACGT 59.828 50.000 0.00 0.00 0.00 4.49
2496 2776 3.149196 CCTCTCTCTCAGGCTAGATCAC 58.851 54.545 0.00 0.00 0.00 3.06
2497 2777 3.052329 TCCTCTCTCTCAGGCTAGATCA 58.948 50.000 0.00 0.00 0.00 2.92
2512 2803 1.070445 CCATGACCATGAGCTCCTCTC 59.930 57.143 12.15 1.12 41.20 3.20
2527 2818 2.137702 ACCATCACCATCCATCCATGA 58.862 47.619 0.00 0.00 0.00 3.07
2556 2847 0.734889 GCGTTGTAATCCTGCAGCAT 59.265 50.000 8.66 0.00 0.00 3.79
2654 2945 0.246360 TGGAGTGCCACTGTATGACG 59.754 55.000 0.00 0.00 39.92 4.35
2774 3092 4.012374 AGAAATGTTGCTACTGTCCATGG 58.988 43.478 4.97 4.97 0.00 3.66
2775 3093 4.696877 TGAGAAATGTTGCTACTGTCCATG 59.303 41.667 0.00 0.00 0.00 3.66
2776 3094 4.910195 TGAGAAATGTTGCTACTGTCCAT 58.090 39.130 0.00 0.00 0.00 3.41
2777 3095 4.202357 ACTGAGAAATGTTGCTACTGTCCA 60.202 41.667 0.00 0.00 0.00 4.02
2778 3096 4.319177 ACTGAGAAATGTTGCTACTGTCC 58.681 43.478 0.00 0.00 0.00 4.02
2779 3097 5.683859 CAACTGAGAAATGTTGCTACTGTC 58.316 41.667 0.00 0.00 37.36 3.51
2789 3107 6.006449 AGATACCAAAGCAACTGAGAAATGT 58.994 36.000 0.00 0.00 0.00 2.71
2790 3108 6.506500 AGATACCAAAGCAACTGAGAAATG 57.493 37.500 0.00 0.00 0.00 2.32
2791 3109 5.352569 CGAGATACCAAAGCAACTGAGAAAT 59.647 40.000 0.00 0.00 0.00 2.17
2792 3110 4.690748 CGAGATACCAAAGCAACTGAGAAA 59.309 41.667 0.00 0.00 0.00 2.52
2793 3111 4.021456 TCGAGATACCAAAGCAACTGAGAA 60.021 41.667 0.00 0.00 0.00 2.87
2819 3139 3.056107 GGTTGTCAGTGCCATGAGTAGTA 60.056 47.826 0.00 0.00 0.00 1.82
2820 3140 2.289694 GGTTGTCAGTGCCATGAGTAGT 60.290 50.000 0.00 0.00 0.00 2.73
2821 3141 2.289631 TGGTTGTCAGTGCCATGAGTAG 60.290 50.000 0.00 0.00 0.00 2.57
2822 3142 1.696884 TGGTTGTCAGTGCCATGAGTA 59.303 47.619 0.00 0.00 0.00 2.59
2823 3143 0.473755 TGGTTGTCAGTGCCATGAGT 59.526 50.000 0.00 0.00 0.00 3.41
2824 3144 0.877071 GTGGTTGTCAGTGCCATGAG 59.123 55.000 0.00 0.00 34.52 2.90
2825 3145 0.182299 TGTGGTTGTCAGTGCCATGA 59.818 50.000 0.00 0.00 34.52 3.07
2826 3146 1.250328 ATGTGGTTGTCAGTGCCATG 58.750 50.000 0.00 0.00 34.52 3.66
2827 3147 2.436417 GTATGTGGTTGTCAGTGCCAT 58.564 47.619 0.00 0.00 34.52 4.40
2828 3148 1.875996 CGTATGTGGTTGTCAGTGCCA 60.876 52.381 0.00 0.00 0.00 4.92
2829 3149 0.796312 CGTATGTGGTTGTCAGTGCC 59.204 55.000 0.00 0.00 0.00 5.01
2832 3152 3.428452 CGTATCCGTATGTGGTTGTCAGT 60.428 47.826 0.00 0.00 0.00 3.41
2835 3155 2.159198 ACCGTATCCGTATGTGGTTGTC 60.159 50.000 0.00 0.00 0.00 3.18
2836 3156 1.826720 ACCGTATCCGTATGTGGTTGT 59.173 47.619 0.00 0.00 0.00 3.32
2838 3158 2.101783 TCACCGTATCCGTATGTGGTT 58.898 47.619 0.00 0.00 0.00 3.67
2841 3161 2.543031 CCTGTCACCGTATCCGTATGTG 60.543 54.545 0.00 0.00 0.00 3.21
2842 3162 1.679680 CCTGTCACCGTATCCGTATGT 59.320 52.381 0.00 0.00 0.00 2.29
2843 3163 1.951602 TCCTGTCACCGTATCCGTATG 59.048 52.381 0.00 0.00 0.00 2.39
2844 3164 2.353357 TCCTGTCACCGTATCCGTAT 57.647 50.000 0.00 0.00 0.00 3.06
2845 3165 2.127271 TTCCTGTCACCGTATCCGTA 57.873 50.000 0.00 0.00 0.00 4.02
2846 3166 1.259609 TTTCCTGTCACCGTATCCGT 58.740 50.000 0.00 0.00 0.00 4.69
2847 3167 2.373540 TTTTCCTGTCACCGTATCCG 57.626 50.000 0.00 0.00 0.00 4.18
2886 3238 1.165284 CCTCCTCGTACTCGGTAGCC 61.165 65.000 0.00 0.00 37.69 3.93
3045 3397 5.448360 GCAAGCAAAGAATGAGAGGTGATAC 60.448 44.000 0.00 0.00 0.00 2.24
3046 3398 4.637534 GCAAGCAAAGAATGAGAGGTGATA 59.362 41.667 0.00 0.00 0.00 2.15
3047 3399 3.442977 GCAAGCAAAGAATGAGAGGTGAT 59.557 43.478 0.00 0.00 0.00 3.06
3120 3492 3.885901 ACTGAAGCAAAGAAACTCCTTCC 59.114 43.478 0.00 0.00 34.21 3.46
3175 3547 7.173218 AGGAAACCATATGATATGTTTGTAGCG 59.827 37.037 11.20 0.00 0.00 4.26
3179 3551 8.821686 TCAAGGAAACCATATGATATGTTTGT 57.178 30.769 11.20 0.09 0.00 2.83
3250 3622 4.761739 TCAGCTCAACACCTAATTGAAAGG 59.238 41.667 0.00 0.00 35.70 3.11
3270 3648 1.174783 AAGGCAATGCTCAAGCTCAG 58.825 50.000 4.82 0.00 42.66 3.35
3395 3787 1.730501 CACATGTGCATCTCCGAAGT 58.269 50.000 13.94 0.00 0.00 3.01
3845 4299 1.691195 GGAGGGAGGCTACTCTTGGC 61.691 65.000 15.65 0.00 43.46 4.52
3850 4304 1.551329 CCTATGGGAGGGAGGCTACTC 60.551 61.905 9.54 9.54 42.39 2.59
3899 4357 1.171308 ATCTGCATGCAACACTGACC 58.829 50.000 22.88 0.00 0.00 4.02
3902 4360 3.004862 TCTGTATCTGCATGCAACACTG 58.995 45.455 22.88 20.24 0.00 3.66
3912 4370 4.646492 TGCTCTTCTGTATCTGTATCTGCA 59.354 41.667 0.00 0.00 0.00 4.41
3913 4371 5.193663 TGCTCTTCTGTATCTGTATCTGC 57.806 43.478 0.00 0.00 0.00 4.26
3914 4372 6.700960 CCTTTGCTCTTCTGTATCTGTATCTG 59.299 42.308 0.00 0.00 0.00 2.90
3915 4373 6.183360 CCCTTTGCTCTTCTGTATCTGTATCT 60.183 42.308 0.00 0.00 0.00 1.98
3916 4374 5.988561 CCCTTTGCTCTTCTGTATCTGTATC 59.011 44.000 0.00 0.00 0.00 2.24
3917 4375 5.686124 GCCCTTTGCTCTTCTGTATCTGTAT 60.686 44.000 0.00 0.00 36.87 2.29
3934 4397 3.381272 TGAGTTCTTTCAACTGCCCTTTG 59.619 43.478 0.00 0.00 0.00 2.77
3982 4445 5.118286 ACCAGCAGAAAATTGGTGAAAAAG 58.882 37.500 6.76 0.00 46.65 2.27
3993 4457 3.857010 GCTTTACGCAACCAGCAGAAAAT 60.857 43.478 0.00 0.00 46.13 1.82
4026 4490 6.970043 TGAACAAAAAGAATCACAGGTTAACG 59.030 34.615 0.00 0.00 0.00 3.18
4131 4597 7.664082 AAACTTGATCTACACATCTCACAAG 57.336 36.000 0.00 0.00 39.17 3.16
4197 4663 4.038522 AGCATGCGTGAAGAGTGTATATCT 59.961 41.667 13.01 0.00 0.00 1.98
4204 4670 1.002366 GGTAGCATGCGTGAAGAGTG 58.998 55.000 13.01 0.00 0.00 3.51
4205 4671 0.898320 AGGTAGCATGCGTGAAGAGT 59.102 50.000 13.01 0.00 0.00 3.24
4206 4672 1.284657 CAGGTAGCATGCGTGAAGAG 58.715 55.000 13.01 0.00 38.93 2.85
4207 4673 0.608130 ACAGGTAGCATGCGTGAAGA 59.392 50.000 13.01 0.00 38.93 2.87
4208 4674 2.293677 TACAGGTAGCATGCGTGAAG 57.706 50.000 13.01 6.50 38.93 3.02
4209 4675 2.232696 TCTTACAGGTAGCATGCGTGAA 59.767 45.455 13.01 0.00 38.93 3.18
4210 4676 1.822371 TCTTACAGGTAGCATGCGTGA 59.178 47.619 13.01 0.00 38.93 4.35
4211 4677 2.293677 TCTTACAGGTAGCATGCGTG 57.706 50.000 13.01 11.09 42.35 5.34
4212 4678 2.826428 CATCTTACAGGTAGCATGCGT 58.174 47.619 13.01 6.21 0.00 5.24
4213 4679 1.528586 GCATCTTACAGGTAGCATGCG 59.471 52.381 13.01 0.00 0.00 4.73
4214 4680 1.528586 CGCATCTTACAGGTAGCATGC 59.471 52.381 10.51 10.51 32.74 4.06
4215 4681 3.097877 TCGCATCTTACAGGTAGCATG 57.902 47.619 0.00 0.00 0.00 4.06
4216 4682 3.321968 TCATCGCATCTTACAGGTAGCAT 59.678 43.478 0.00 0.00 0.00 3.79
4217 4683 2.693074 TCATCGCATCTTACAGGTAGCA 59.307 45.455 0.00 0.00 0.00 3.49
4218 4684 3.371102 TCATCGCATCTTACAGGTAGC 57.629 47.619 0.00 0.00 0.00 3.58
4219 4685 4.151335 GCAATCATCGCATCTTACAGGTAG 59.849 45.833 0.00 0.00 0.00 3.18
4220 4686 4.058124 GCAATCATCGCATCTTACAGGTA 58.942 43.478 0.00 0.00 0.00 3.08
4221 4687 2.874701 GCAATCATCGCATCTTACAGGT 59.125 45.455 0.00 0.00 0.00 4.00
4222 4688 2.874086 TGCAATCATCGCATCTTACAGG 59.126 45.455 0.00 0.00 33.55 4.00
4233 4699 3.059393 AGCAATACATCGTGCAATCATCG 60.059 43.478 0.00 0.00 43.42 3.84
4286 4752 2.751688 GTCCGTGGCCCACCTTTA 59.248 61.111 8.62 0.00 36.63 1.85
4307 4773 5.507650 CCGCCTCCTAGTTTCTTGTATAGTC 60.508 48.000 0.00 0.00 0.00 2.59
4318 4784 3.408853 GGGCCCGCCTCCTAGTTT 61.409 66.667 5.69 0.00 36.10 2.66
4442 4912 3.048600 TCATGACTAAGGGCTTGCCTAT 58.951 45.455 11.71 3.55 0.00 2.57
4456 4926 8.274322 TCCCAACAATTTGTAGATATCATGACT 58.726 33.333 5.32 0.00 0.00 3.41
4484 4954 7.444183 CCATATTCGTGTTTTACATGTCCCTAT 59.556 37.037 0.00 0.00 36.53 2.57
4587 5057 2.439701 CGGCGGTCTACCTCTCCA 60.440 66.667 0.00 0.00 0.00 3.86
4614 5084 3.056458 CCACGGTGGTCTACTGCA 58.944 61.111 19.15 0.00 39.39 4.41
4641 5111 0.773644 TCAGGAGCTTTCTTGCCCTT 59.226 50.000 0.00 0.00 33.47 3.95


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

AutoCloner maintained by Alex Coulton.