Multiple sequence alignment - TraesCS5B01G281500

Loading Multiple Alignment...

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 TraesCS5B01G281500 chr5B 100.000 2555 0 0 1 2555 466769657 466772211 0.000000e+00 4719.0
1 TraesCS5B01G281500 chr5B 93.676 253 12 2 6 254 470115890 470116142 2.400000e-100 375.0
2 TraesCS5B01G281500 chr5A 92.274 1618 92 12 213 1807 491253178 491254785 0.000000e+00 2265.0
3 TraesCS5B01G281500 chr5A 78.384 1027 186 20 684 1688 491241343 491242355 3.590000e-178 634.0
4 TraesCS5B01G281500 chr5A 91.534 378 26 5 1873 2245 491254782 491255158 1.360000e-142 516.0
5 TraesCS5B01G281500 chr5A 92.063 252 12 4 7 254 493376884 493377131 5.230000e-92 348.0
6 TraesCS5B01G281500 chr5A 93.636 220 10 2 6 221 491252226 491252445 2.450000e-85 326.0
7 TraesCS5B01G281500 chr5A 88.421 95 9 2 2227 2320 491285890 491285983 2.080000e-21 113.0
8 TraesCS5B01G281500 chr5A 92.308 52 3 1 2310 2361 438927816 438927866 3.530000e-09 73.1
9 TraesCS5B01G281500 chr5D 91.146 1344 82 15 504 1832 388093062 388094383 0.000000e+00 1788.0
10 TraesCS5B01G281500 chr5D 75.738 1389 265 40 336 1688 388053039 388054391 1.290000e-177 632.0
11 TraesCS5B01G281500 chr5D 90.119 253 15 4 258 507 388092725 388092970 1.140000e-83 320.0
12 TraesCS5B01G281500 chr5D 90.110 182 16 2 1921 2101 388094383 388094563 4.250000e-58 235.0
13 TraesCS5B01G281500 chr5D 90.230 174 16 1 2150 2322 388094981 388095154 2.560000e-55 226.0
14 TraesCS5B01G281500 chr5D 73.926 349 56 28 6 335 388052546 388052878 9.670000e-20 108.0
15 TraesCS5B01G281500 chr5D 100.000 28 0 0 2097 2124 388094571 388094598 5.000000e-03 52.8
16 TraesCS5B01G281500 chr1D 95.385 65 0 1 2323 2384 233910362 233910298 1.620000e-17 100.0
17 TraesCS5B01G281500 chr7A 97.778 45 1 0 2317 2361 21185662 21185618 7.580000e-11 78.7
18 TraesCS5B01G281500 chr7A 86.957 69 5 4 2294 2361 689905990 689906055 9.800000e-10 75.0
19 TraesCS5B01G281500 chr7A 90.741 54 4 1 2309 2361 66638204 66638151 1.270000e-08 71.3
20 TraesCS5B01G281500 chr3B 97.778 45 1 0 2317 2361 590450769 590450813 7.580000e-11 78.7
21 TraesCS5B01G281500 chr4D 94.000 50 2 1 2312 2361 331632373 331632421 9.800000e-10 75.0
22 TraesCS5B01G281500 chr3A 87.500 64 6 2 2300 2361 259336846 259336909 3.530000e-09 73.1
23 TraesCS5B01G281500 chr1A 84.615 78 7 5 2287 2361 25334087 25334162 3.530000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G281500 chr5B 466769657 466772211 2554 False 4719.000000 4719 100.000000 1 2555 1 chr5B.!!$F1 2554
1 TraesCS5B01G281500 chr5A 491252226 491255158 2932 False 1035.666667 2265 92.481333 6 2245 3 chr5A.!!$F5 2239
2 TraesCS5B01G281500 chr5A 491241343 491242355 1012 False 634.000000 634 78.384000 684 1688 1 chr5A.!!$F2 1004
3 TraesCS5B01G281500 chr5D 388092725 388095154 2429 False 524.360000 1788 92.321000 258 2322 5 chr5D.!!$F2 2064
4 TraesCS5B01G281500 chr5D 388052546 388054391 1845 False 370.000000 632 74.832000 6 1688 2 chr5D.!!$F1 1682

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
140 154 3.896888 TGTTTAAGTAGACCGGACCTTGA 59.103 43.478 9.46 0.00 0.00 3.02 F
1181 2233 0.969149 AACATCTCTGGCGACTGTGA 59.031 50.000 2.22 2.22 36.46 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 2488 0.038892 GAAGGTACAACGACGCTGGA 60.039 55.0 2.97 0.0 0.00 3.86 R
2416 3852 0.038166 GGAGTGCCCAATCTGAACCA 59.962 55.0 0.00 0.0 34.14 3.67 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
83 88 6.042777 CGCTCCAAAGTCTATGATTTAGACA 58.957 40.000 13.56 0.00 44.66 3.41
84 89 6.703607 CGCTCCAAAGTCTATGATTTAGACAT 59.296 38.462 13.56 1.00 44.66 3.06
140 154 3.896888 TGTTTAAGTAGACCGGACCTTGA 59.103 43.478 9.46 0.00 0.00 3.02
207 221 9.424319 ACATTATTCACTTCGTAATATAGGCTG 57.576 33.333 0.00 0.00 0.00 4.85
209 223 6.665992 ATTCACTTCGTAATATAGGCTGGA 57.334 37.500 0.00 0.00 0.00 3.86
210 224 5.449107 TCACTTCGTAATATAGGCTGGAC 57.551 43.478 0.00 0.00 0.00 4.02
241 997 6.484643 ACATCCATGCATAGAACACTACATTC 59.515 38.462 0.00 0.00 0.00 2.67
281 1038 5.083533 ACAGCCTCTCTCTTTTACATCTG 57.916 43.478 0.00 0.00 0.00 2.90
360 1280 8.560374 AGTAAACATAAAGCTCAGTTTTCACTC 58.440 33.333 9.89 0.95 35.90 3.51
412 1332 6.560253 ACTTTACTGTCATTGTTCCATGAC 57.440 37.500 6.84 6.84 45.35 3.06
416 1338 7.581213 TTACTGTCATTGTTCCATGACTTTT 57.419 32.000 13.50 2.81 45.35 2.27
836 1881 5.410746 CACCATTATGCACTCTGTATCCATC 59.589 44.000 0.00 0.00 0.00 3.51
914 1964 9.859427 ATGTTTTTACATGTGAACCATCATAAG 57.141 29.630 9.11 0.00 38.01 1.73
923 1973 6.591935 TGTGAACCATCATAAGGGAAGTATC 58.408 40.000 0.00 0.00 38.01 2.24
1035 2087 4.767928 CCTAGGCGAGGGATATATATGGAC 59.232 50.000 5.64 0.00 42.39 4.02
1047 2099 7.374272 GGATATATATGGACGATGATGGTCTG 58.626 42.308 7.51 0.00 34.82 3.51
1181 2233 0.969149 AACATCTCTGGCGACTGTGA 59.031 50.000 2.22 2.22 36.46 3.58
1240 2292 1.267121 GGTTGAGGCCACAGTAGAGA 58.733 55.000 5.01 0.00 0.00 3.10
1250 2302 5.843421 AGGCCACAGTAGAGATTCTCATATT 59.157 40.000 15.83 0.00 32.06 1.28
1277 2329 1.331756 GCAGAGCGGTTTCCATATGTG 59.668 52.381 1.24 0.00 0.00 3.21
1386 2438 1.116536 TTGCCGTAGTGAGGTGGTCA 61.117 55.000 0.00 0.00 0.00 4.02
1401 2453 3.374058 GGTGGTCATCCATACGTTTGAAG 59.626 47.826 7.64 0.00 46.20 3.02
1408 2460 6.147164 GTCATCCATACGTTTGAAGTTCAAGA 59.853 38.462 17.36 10.43 37.70 3.02
1417 2469 5.791974 CGTTTGAAGTTCAAGATATGCACAG 59.208 40.000 17.36 5.47 37.70 3.66
1418 2470 6.347644 CGTTTGAAGTTCAAGATATGCACAGA 60.348 38.462 17.36 0.00 37.70 3.41
1436 2488 2.036475 CAGAATCATCCGGATCCGAGTT 59.964 50.000 35.42 19.90 42.83 3.01
1440 2492 0.032678 CATCCGGATCCGAGTTCCAG 59.967 60.000 35.42 16.45 42.83 3.86
1539 2600 1.733399 GGTCACTTGGTCGACGCTC 60.733 63.158 9.92 0.00 32.74 5.03
1566 2627 0.393537 CCTGGTAGCTTTCCTGGCTG 60.394 60.000 16.30 0.00 40.52 4.85
1620 2683 0.988832 AGCGGACCAAGGGATTAACA 59.011 50.000 0.00 0.00 0.00 2.41
1626 2689 4.520179 GGACCAAGGGATTAACAACGTAT 58.480 43.478 0.00 0.00 0.00 3.06
1674 2738 3.123621 GTGACAAGCTTGGAGTGTAATCG 59.876 47.826 29.18 0.86 0.00 3.34
1678 2742 3.678056 AGCTTGGAGTGTAATCGAACA 57.322 42.857 0.00 0.00 0.00 3.18
1693 2757 8.118607 TGTAATCGAACAGTTGTACTATCTACG 58.881 37.037 0.00 0.00 0.00 3.51
1734 2798 3.127533 GCCACGGATGCTCCACAC 61.128 66.667 3.57 0.00 35.91 3.82
1735 2799 2.665000 CCACGGATGCTCCACACT 59.335 61.111 3.57 0.00 35.91 3.55
1736 2800 1.003355 CCACGGATGCTCCACACTT 60.003 57.895 3.57 0.00 35.91 3.16
1737 2801 1.021390 CCACGGATGCTCCACACTTC 61.021 60.000 3.57 0.00 35.91 3.01
1738 2802 1.021390 CACGGATGCTCCACACTTCC 61.021 60.000 3.57 0.00 35.91 3.46
1739 2803 1.296392 CGGATGCTCCACACTTCCA 59.704 57.895 3.57 0.00 35.91 3.53
1740 2804 1.021390 CGGATGCTCCACACTTCCAC 61.021 60.000 3.57 0.00 35.91 4.02
1741 2805 0.036732 GGATGCTCCACACTTCCACA 59.963 55.000 0.00 0.00 36.28 4.17
1745 2809 0.394565 GCTCCACACTTCCACAGTCT 59.605 55.000 0.00 0.00 30.92 3.24
1749 2813 0.947244 CACACTTCCACAGTCTTGCC 59.053 55.000 0.00 0.00 30.92 4.52
1778 2842 7.123355 TCCACATTTTGTTTCTTCTTTCCAT 57.877 32.000 0.00 0.00 0.00 3.41
1807 2871 3.004944 GGCAACACGGATTAGGTCAAAAA 59.995 43.478 0.00 0.00 0.00 1.94
1808 2872 3.978855 GCAACACGGATTAGGTCAAAAAC 59.021 43.478 0.00 0.00 0.00 2.43
1831 2896 3.664320 TGGAGGATATTTCCCAGCTACA 58.336 45.455 0.00 0.00 43.76 2.74
1832 2897 3.391296 TGGAGGATATTTCCCAGCTACAC 59.609 47.826 0.00 0.00 43.76 2.90
1833 2898 3.391296 GGAGGATATTTCCCAGCTACACA 59.609 47.826 0.00 0.00 43.76 3.72
1834 2899 4.042187 GGAGGATATTTCCCAGCTACACAT 59.958 45.833 0.00 0.00 43.76 3.21
1835 2900 5.234466 AGGATATTTCCCAGCTACACATC 57.766 43.478 0.00 0.00 43.76 3.06
1836 2901 4.042187 AGGATATTTCCCAGCTACACATCC 59.958 45.833 0.00 0.00 43.76 3.51
1837 2902 4.202461 GGATATTTCCCAGCTACACATCCA 60.202 45.833 0.00 0.00 35.84 3.41
1838 2903 2.489938 TTTCCCAGCTACACATCCAC 57.510 50.000 0.00 0.00 0.00 4.02
1839 2904 1.357137 TTCCCAGCTACACATCCACA 58.643 50.000 0.00 0.00 0.00 4.17
1840 2905 0.904649 TCCCAGCTACACATCCACAG 59.095 55.000 0.00 0.00 0.00 3.66
1841 2906 0.107508 CCCAGCTACACATCCACAGG 60.108 60.000 0.00 0.00 0.00 4.00
1842 2907 0.904649 CCAGCTACACATCCACAGGA 59.095 55.000 0.00 0.00 35.55 3.86
1843 2908 1.487976 CCAGCTACACATCCACAGGAT 59.512 52.381 0.00 0.00 44.21 3.24
1852 2917 3.895025 CCACAGGATGGCTTCACG 58.105 61.111 2.60 0.00 43.24 4.35
1853 2918 1.746615 CCACAGGATGGCTTCACGG 60.747 63.158 2.60 0.00 43.24 4.94
1854 2919 1.003355 CACAGGATGGCTTCACGGT 60.003 57.895 2.60 0.00 43.62 4.83
1855 2920 1.003355 ACAGGATGGCTTCACGGTG 60.003 57.895 0.56 0.56 43.62 4.94
1856 2921 2.045926 AGGATGGCTTCACGGTGC 60.046 61.111 2.51 0.00 0.00 5.01
1857 2922 2.359850 GGATGGCTTCACGGTGCA 60.360 61.111 2.51 0.00 0.00 4.57
1858 2923 1.750399 GGATGGCTTCACGGTGCAT 60.750 57.895 2.51 0.81 0.00 3.96
1859 2924 1.430632 GATGGCTTCACGGTGCATG 59.569 57.895 2.51 0.00 0.00 4.06
1860 2925 1.002257 ATGGCTTCACGGTGCATGA 60.002 52.632 2.51 0.00 0.00 3.07
1861 2926 1.028330 ATGGCTTCACGGTGCATGAG 61.028 55.000 2.51 0.28 0.00 2.90
1862 2927 1.375908 GGCTTCACGGTGCATGAGA 60.376 57.895 2.51 0.00 0.00 3.27
1863 2928 0.955428 GGCTTCACGGTGCATGAGAA 60.955 55.000 2.51 0.00 0.00 2.87
1864 2929 0.445436 GCTTCACGGTGCATGAGAAG 59.555 55.000 18.28 18.28 37.19 2.85
1865 2930 1.941209 GCTTCACGGTGCATGAGAAGA 60.941 52.381 23.43 3.64 36.52 2.87
1866 2931 2.416747 CTTCACGGTGCATGAGAAGAA 58.583 47.619 17.95 6.29 36.52 2.52
1867 2932 2.768253 TCACGGTGCATGAGAAGAAT 57.232 45.000 2.51 0.00 0.00 2.40
1868 2933 3.057969 TCACGGTGCATGAGAAGAATT 57.942 42.857 2.51 0.00 0.00 2.17
1869 2934 2.743664 TCACGGTGCATGAGAAGAATTG 59.256 45.455 2.51 0.00 0.00 2.32
1870 2935 2.086869 ACGGTGCATGAGAAGAATTGG 58.913 47.619 0.00 0.00 0.00 3.16
1871 2936 2.290260 ACGGTGCATGAGAAGAATTGGA 60.290 45.455 0.00 0.00 0.00 3.53
1872 2937 2.749076 CGGTGCATGAGAAGAATTGGAA 59.251 45.455 0.00 0.00 0.00 3.53
1873 2938 3.191162 CGGTGCATGAGAAGAATTGGAAA 59.809 43.478 0.00 0.00 0.00 3.13
1874 2939 4.321156 CGGTGCATGAGAAGAATTGGAAAA 60.321 41.667 0.00 0.00 0.00 2.29
1875 2940 5.540911 GGTGCATGAGAAGAATTGGAAAAA 58.459 37.500 0.00 0.00 0.00 1.94
1876 2941 6.168389 GGTGCATGAGAAGAATTGGAAAAAT 58.832 36.000 0.00 0.00 0.00 1.82
1895 2960 7.148407 GGAAAAATGAGAGTGAACGATGTACAT 60.148 37.037 8.43 8.43 0.00 2.29
1917 2982 6.014242 ACATGACTCCTGTTTCTGACTGATTA 60.014 38.462 0.00 0.00 0.00 1.75
2001 3066 4.107622 GGAAGCCATTCATGACGAAATTG 58.892 43.478 0.00 0.00 37.12 2.32
2083 3149 2.337170 CAGTACCGCGTGTGGTGA 59.663 61.111 15.13 0.00 43.68 4.02
2089 3155 2.689785 CCGCGTGTGGTGATTGCAT 61.690 57.895 4.92 0.00 0.00 3.96
2134 3212 5.622914 GCTGAGCTTTTGAGCCATAATTGAA 60.623 40.000 0.00 0.00 34.90 2.69
2155 3590 7.601705 TGAAGGGAGAATCTTGTTGATTTTT 57.398 32.000 0.00 0.00 44.70 1.94
2238 3673 2.354303 CGGGTGGCTTGTGAGTGTATTA 60.354 50.000 0.00 0.00 0.00 0.98
2246 3681 7.962918 GTGGCTTGTGAGTGTATTAATGTTTAG 59.037 37.037 0.00 0.00 0.00 1.85
2269 3704 5.104527 AGACCGGAGTATTTGGAAATGATCA 60.105 40.000 9.46 0.00 0.00 2.92
2322 3758 2.315925 TCCTAGCTTGGAGAAATGCG 57.684 50.000 13.28 0.00 0.00 4.73
2323 3759 1.134401 TCCTAGCTTGGAGAAATGCGG 60.134 52.381 13.28 0.00 0.00 5.69
2324 3760 1.134401 CCTAGCTTGGAGAAATGCGGA 60.134 52.381 8.73 0.00 0.00 5.54
2325 3761 2.632377 CTAGCTTGGAGAAATGCGGAA 58.368 47.619 0.00 0.00 0.00 4.30
2326 3762 1.457346 AGCTTGGAGAAATGCGGAAG 58.543 50.000 0.00 0.00 0.00 3.46
2327 3763 0.453390 GCTTGGAGAAATGCGGAAGG 59.547 55.000 0.00 0.00 0.00 3.46
2328 3764 1.098050 CTTGGAGAAATGCGGAAGGG 58.902 55.000 0.00 0.00 0.00 3.95
2329 3765 0.323360 TTGGAGAAATGCGGAAGGGG 60.323 55.000 0.00 0.00 0.00 4.79
2330 3766 1.204786 TGGAGAAATGCGGAAGGGGA 61.205 55.000 0.00 0.00 0.00 4.81
2331 3767 0.464554 GGAGAAATGCGGAAGGGGAG 60.465 60.000 0.00 0.00 0.00 4.30
2332 3768 1.077429 AGAAATGCGGAAGGGGAGC 60.077 57.895 0.00 0.00 0.00 4.70
2333 3769 2.043953 AAATGCGGAAGGGGAGCC 60.044 61.111 0.00 0.00 0.00 4.70
2334 3770 2.558380 GAAATGCGGAAGGGGAGCCT 62.558 60.000 0.00 0.00 0.00 4.58
2335 3771 2.155197 AAATGCGGAAGGGGAGCCTT 62.155 55.000 0.00 0.00 0.00 4.35
2336 3772 2.843912 AATGCGGAAGGGGAGCCTTG 62.844 60.000 0.00 0.00 0.00 3.61
2337 3773 4.803908 GCGGAAGGGGAGCCTTGG 62.804 72.222 0.00 0.00 0.00 3.61
2338 3774 4.803908 CGGAAGGGGAGCCTTGGC 62.804 72.222 2.97 2.97 0.00 4.52
2339 3775 4.803908 GGAAGGGGAGCCTTGGCG 62.804 72.222 5.95 0.00 0.00 5.69
2347 3783 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2348 3784 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2349 3785 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2350 3786 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2351 3787 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2352 3788 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2353 3789 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2358 3794 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2359 3795 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2360 3796 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2361 3797 1.351017 AGTGGTAAAGCTGCTGCCTTA 59.649 47.619 12.44 7.26 40.80 2.69
2362 3798 1.740025 GTGGTAAAGCTGCTGCCTTAG 59.260 52.381 12.44 0.00 40.80 2.18
2373 3809 1.303309 CTGCCTTAGCTACATGCACC 58.697 55.000 6.87 0.00 45.94 5.01
2374 3810 0.461870 TGCCTTAGCTACATGCACCG 60.462 55.000 6.87 0.00 45.94 4.94
2375 3811 1.160329 GCCTTAGCTACATGCACCGG 61.160 60.000 0.00 0.00 45.94 5.28
2376 3812 0.532862 CCTTAGCTACATGCACCGGG 60.533 60.000 6.32 0.00 45.94 5.73
2377 3813 1.153249 TTAGCTACATGCACCGGGC 60.153 57.895 6.32 7.25 45.94 6.13
2378 3814 1.622607 TTAGCTACATGCACCGGGCT 61.623 55.000 6.32 4.38 45.94 5.19
2379 3815 2.310327 TAGCTACATGCACCGGGCTG 62.310 60.000 6.32 9.21 45.94 4.85
2380 3816 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
2381 3817 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
2398 3834 2.094675 TGCCCTAGCTTGAAGAAATGC 58.905 47.619 0.00 0.00 40.80 3.56
2399 3835 2.094675 GCCCTAGCTTGAAGAAATGCA 58.905 47.619 0.00 0.00 35.50 3.96
2400 3836 2.159324 GCCCTAGCTTGAAGAAATGCAC 60.159 50.000 0.00 0.00 35.50 4.57
2401 3837 3.084039 CCCTAGCTTGAAGAAATGCACA 58.916 45.455 0.00 0.00 0.00 4.57
2402 3838 3.698040 CCCTAGCTTGAAGAAATGCACAT 59.302 43.478 0.00 0.00 0.00 3.21
2403 3839 4.439700 CCCTAGCTTGAAGAAATGCACATG 60.440 45.833 0.00 0.00 0.00 3.21
2404 3840 4.397103 CCTAGCTTGAAGAAATGCACATGA 59.603 41.667 0.00 0.00 0.00 3.07
2405 3841 5.067413 CCTAGCTTGAAGAAATGCACATGAT 59.933 40.000 0.00 0.00 0.00 2.45
2406 3842 4.744570 AGCTTGAAGAAATGCACATGATG 58.255 39.130 0.00 0.00 0.00 3.07
2407 3843 4.219944 AGCTTGAAGAAATGCACATGATGT 59.780 37.500 0.00 0.00 0.00 3.06
2408 3844 4.927425 GCTTGAAGAAATGCACATGATGTT 59.073 37.500 0.00 0.00 0.00 2.71
2409 3845 5.163992 GCTTGAAGAAATGCACATGATGTTG 60.164 40.000 0.00 0.00 0.00 3.33
2410 3846 5.456548 TGAAGAAATGCACATGATGTTGT 57.543 34.783 0.00 0.00 0.00 3.32
2411 3847 6.572167 TGAAGAAATGCACATGATGTTGTA 57.428 33.333 0.00 0.00 0.00 2.41
2412 3848 7.160547 TGAAGAAATGCACATGATGTTGTAT 57.839 32.000 0.00 0.00 0.00 2.29
2413 3849 7.604549 TGAAGAAATGCACATGATGTTGTATT 58.395 30.769 0.00 0.83 0.00 1.89
2414 3850 7.542824 TGAAGAAATGCACATGATGTTGTATTG 59.457 33.333 0.00 0.00 0.00 1.90
2415 3851 6.334989 AGAAATGCACATGATGTTGTATTGG 58.665 36.000 0.00 0.00 0.00 3.16
2416 3852 5.664294 AATGCACATGATGTTGTATTGGT 57.336 34.783 0.00 0.00 0.00 3.67
2417 3853 4.437772 TGCACATGATGTTGTATTGGTG 57.562 40.909 0.00 0.00 0.00 4.17
2418 3854 3.193056 TGCACATGATGTTGTATTGGTGG 59.807 43.478 0.00 0.00 0.00 4.61
2419 3855 3.193267 GCACATGATGTTGTATTGGTGGT 59.807 43.478 0.00 0.00 0.00 4.16
2420 3856 4.321899 GCACATGATGTTGTATTGGTGGTT 60.322 41.667 0.00 0.00 0.00 3.67
2421 3857 5.401550 CACATGATGTTGTATTGGTGGTTC 58.598 41.667 0.00 0.00 0.00 3.62
2422 3858 5.048154 CACATGATGTTGTATTGGTGGTTCA 60.048 40.000 0.00 0.00 0.00 3.18
2423 3859 5.183713 ACATGATGTTGTATTGGTGGTTCAG 59.816 40.000 0.00 0.00 0.00 3.02
2424 3860 4.979335 TGATGTTGTATTGGTGGTTCAGA 58.021 39.130 0.00 0.00 0.00 3.27
2425 3861 5.569355 TGATGTTGTATTGGTGGTTCAGAT 58.431 37.500 0.00 0.00 0.00 2.90
2426 3862 6.009589 TGATGTTGTATTGGTGGTTCAGATT 58.990 36.000 0.00 0.00 0.00 2.40
2427 3863 5.703978 TGTTGTATTGGTGGTTCAGATTG 57.296 39.130 0.00 0.00 0.00 2.67
2428 3864 4.522405 TGTTGTATTGGTGGTTCAGATTGG 59.478 41.667 0.00 0.00 0.00 3.16
2429 3865 3.696045 TGTATTGGTGGTTCAGATTGGG 58.304 45.455 0.00 0.00 0.00 4.12
2430 3866 1.560505 ATTGGTGGTTCAGATTGGGC 58.439 50.000 0.00 0.00 0.00 5.36
2431 3867 0.187117 TTGGTGGTTCAGATTGGGCA 59.813 50.000 0.00 0.00 0.00 5.36
2432 3868 0.539438 TGGTGGTTCAGATTGGGCAC 60.539 55.000 0.00 0.00 0.00 5.01
2433 3869 0.251341 GGTGGTTCAGATTGGGCACT 60.251 55.000 0.00 0.00 0.00 4.40
2434 3870 1.168714 GTGGTTCAGATTGGGCACTC 58.831 55.000 0.00 0.00 0.00 3.51
2435 3871 0.038166 TGGTTCAGATTGGGCACTCC 59.962 55.000 0.00 0.00 0.00 3.85
2445 3881 4.943822 GGCACTCCCTAGTTGCTC 57.056 61.111 0.00 0.00 31.97 4.26
2446 3882 2.291856 GGCACTCCCTAGTTGCTCT 58.708 57.895 0.00 0.00 31.97 4.09
2447 3883 1.486211 GGCACTCCCTAGTTGCTCTA 58.514 55.000 0.00 0.00 31.97 2.43
2448 3884 2.043227 GGCACTCCCTAGTTGCTCTAT 58.957 52.381 0.00 0.00 31.97 1.98
2449 3885 3.231818 GGCACTCCCTAGTTGCTCTATA 58.768 50.000 0.00 0.00 31.97 1.31
2450 3886 3.257127 GGCACTCCCTAGTTGCTCTATAG 59.743 52.174 0.00 0.00 31.97 1.31
2451 3887 3.257127 GCACTCCCTAGTTGCTCTATAGG 59.743 52.174 0.00 0.00 36.59 2.57
2452 3888 3.257127 CACTCCCTAGTTGCTCTATAGGC 59.743 52.174 0.00 3.21 35.68 3.93
2453 3889 2.829120 CTCCCTAGTTGCTCTATAGGCC 59.171 54.545 0.00 0.00 35.68 5.19
2454 3890 2.179204 TCCCTAGTTGCTCTATAGGCCA 59.821 50.000 5.01 0.00 35.68 5.36
2455 3891 3.177228 CCCTAGTTGCTCTATAGGCCAT 58.823 50.000 5.01 0.00 35.68 4.40
2456 3892 3.196685 CCCTAGTTGCTCTATAGGCCATC 59.803 52.174 5.01 0.00 35.68 3.51
2457 3893 3.834813 CCTAGTTGCTCTATAGGCCATCA 59.165 47.826 5.01 0.00 30.28 3.07
2458 3894 4.469227 CCTAGTTGCTCTATAGGCCATCAT 59.531 45.833 5.01 0.00 30.28 2.45
2459 3895 4.989875 AGTTGCTCTATAGGCCATCATT 57.010 40.909 5.01 0.00 0.00 2.57
2460 3896 6.155221 CCTAGTTGCTCTATAGGCCATCATTA 59.845 42.308 5.01 0.00 30.28 1.90
2461 3897 6.633325 AGTTGCTCTATAGGCCATCATTAT 57.367 37.500 5.01 0.00 0.00 1.28
2462 3898 7.739995 AGTTGCTCTATAGGCCATCATTATA 57.260 36.000 5.01 0.00 0.00 0.98
2463 3899 7.560368 AGTTGCTCTATAGGCCATCATTATAC 58.440 38.462 5.01 0.00 0.00 1.47
2464 3900 7.180946 AGTTGCTCTATAGGCCATCATTATACA 59.819 37.037 5.01 0.00 0.00 2.29
2465 3901 6.878317 TGCTCTATAGGCCATCATTATACAC 58.122 40.000 5.01 0.00 0.00 2.90
2466 3902 6.669591 TGCTCTATAGGCCATCATTATACACT 59.330 38.462 5.01 0.00 0.00 3.55
2467 3903 6.983307 GCTCTATAGGCCATCATTATACACTG 59.017 42.308 5.01 0.00 0.00 3.66
2468 3904 7.147828 GCTCTATAGGCCATCATTATACACTGA 60.148 40.741 5.01 0.00 0.00 3.41
2469 3905 8.298729 TCTATAGGCCATCATTATACACTGAG 57.701 38.462 5.01 0.00 0.00 3.35
2470 3906 4.630644 AGGCCATCATTATACACTGAGG 57.369 45.455 5.01 0.00 0.00 3.86
2471 3907 3.976654 AGGCCATCATTATACACTGAGGT 59.023 43.478 5.01 0.00 0.00 3.85
2472 3908 4.413520 AGGCCATCATTATACACTGAGGTT 59.586 41.667 5.01 0.00 0.00 3.50
2473 3909 4.757149 GGCCATCATTATACACTGAGGTTC 59.243 45.833 0.00 0.00 0.00 3.62
2474 3910 5.368145 GCCATCATTATACACTGAGGTTCA 58.632 41.667 0.00 0.00 0.00 3.18
2483 3919 3.753787 CTGAGGTTCAGGGCCTTTT 57.246 52.632 1.32 0.00 40.71 2.27
2484 3920 1.251251 CTGAGGTTCAGGGCCTTTTG 58.749 55.000 1.32 0.00 40.71 2.44
2485 3921 0.827507 TGAGGTTCAGGGCCTTTTGC 60.828 55.000 1.32 0.00 36.29 3.68
2486 3922 0.540597 GAGGTTCAGGGCCTTTTGCT 60.541 55.000 1.32 0.00 40.92 3.91
2487 3923 0.777446 AGGTTCAGGGCCTTTTGCTA 59.223 50.000 1.32 0.00 40.92 3.49
2488 3924 1.146982 AGGTTCAGGGCCTTTTGCTAA 59.853 47.619 1.32 0.00 40.92 3.09
2489 3925 1.967779 GGTTCAGGGCCTTTTGCTAAA 59.032 47.619 1.32 0.00 40.92 1.85
2490 3926 2.567169 GGTTCAGGGCCTTTTGCTAAAT 59.433 45.455 1.32 0.00 40.92 1.40
2491 3927 3.007940 GGTTCAGGGCCTTTTGCTAAATT 59.992 43.478 1.32 0.00 40.92 1.82
2492 3928 4.221924 GGTTCAGGGCCTTTTGCTAAATTA 59.778 41.667 1.32 0.00 40.92 1.40
2493 3929 5.279758 GGTTCAGGGCCTTTTGCTAAATTAA 60.280 40.000 1.32 0.00 40.92 1.40
2494 3930 5.400066 TCAGGGCCTTTTGCTAAATTAAC 57.600 39.130 1.32 0.00 40.92 2.01
2495 3931 5.083821 TCAGGGCCTTTTGCTAAATTAACT 58.916 37.500 1.32 0.00 40.92 2.24
2496 3932 5.185056 TCAGGGCCTTTTGCTAAATTAACTC 59.815 40.000 1.32 0.00 40.92 3.01
2497 3933 5.047377 CAGGGCCTTTTGCTAAATTAACTCA 60.047 40.000 1.32 0.00 40.92 3.41
2498 3934 5.185828 AGGGCCTTTTGCTAAATTAACTCAG 59.814 40.000 0.00 0.00 40.92 3.35
2499 3935 5.410924 GGCCTTTTGCTAAATTAACTCAGG 58.589 41.667 0.00 0.00 40.92 3.86
2500 3936 5.047306 GGCCTTTTGCTAAATTAACTCAGGT 60.047 40.000 0.00 0.00 40.92 4.00
2501 3937 5.863935 GCCTTTTGCTAAATTAACTCAGGTG 59.136 40.000 0.00 0.00 36.87 4.00
2502 3938 5.863935 CCTTTTGCTAAATTAACTCAGGTGC 59.136 40.000 0.00 0.00 0.00 5.01
2503 3939 5.385509 TTTGCTAAATTAACTCAGGTGCC 57.614 39.130 0.00 0.00 0.00 5.01
2504 3940 4.301072 TGCTAAATTAACTCAGGTGCCT 57.699 40.909 0.00 0.00 0.00 4.75
2505 3941 4.662278 TGCTAAATTAACTCAGGTGCCTT 58.338 39.130 0.00 0.00 0.00 4.35
2506 3942 4.458989 TGCTAAATTAACTCAGGTGCCTTG 59.541 41.667 0.00 0.00 0.00 3.61
2507 3943 4.142381 GCTAAATTAACTCAGGTGCCTTGG 60.142 45.833 0.00 0.00 0.00 3.61
2508 3944 2.514458 ATTAACTCAGGTGCCTTGGG 57.486 50.000 0.00 0.00 0.00 4.12
2509 3945 1.145571 TTAACTCAGGTGCCTTGGGT 58.854 50.000 0.00 0.00 0.00 4.51
2510 3946 0.690762 TAACTCAGGTGCCTTGGGTC 59.309 55.000 0.00 0.00 0.00 4.46
2511 3947 2.069165 AACTCAGGTGCCTTGGGTCC 62.069 60.000 0.00 0.00 0.00 4.46
2512 3948 3.256960 TCAGGTGCCTTGGGTCCC 61.257 66.667 0.00 0.00 0.00 4.46
2513 3949 3.260100 CAGGTGCCTTGGGTCCCT 61.260 66.667 10.00 0.00 0.00 4.20
2514 3950 2.452491 AGGTGCCTTGGGTCCCTT 60.452 61.111 10.00 0.00 0.00 3.95
2515 3951 1.151677 AGGTGCCTTGGGTCCCTTA 60.152 57.895 10.00 0.00 0.00 2.69
2516 3952 0.774491 AGGTGCCTTGGGTCCCTTAA 60.774 55.000 10.00 0.00 0.00 1.85
2517 3953 0.113580 GGTGCCTTGGGTCCCTTAAA 59.886 55.000 10.00 0.00 0.00 1.52
2518 3954 1.273041 GGTGCCTTGGGTCCCTTAAAT 60.273 52.381 10.00 0.00 0.00 1.40
2519 3955 2.536066 GTGCCTTGGGTCCCTTAAATT 58.464 47.619 10.00 0.00 0.00 1.82
2520 3956 2.903784 GTGCCTTGGGTCCCTTAAATTT 59.096 45.455 10.00 0.00 0.00 1.82
2521 3957 3.326588 GTGCCTTGGGTCCCTTAAATTTT 59.673 43.478 10.00 0.00 0.00 1.82
2522 3958 3.580895 TGCCTTGGGTCCCTTAAATTTTC 59.419 43.478 10.00 0.00 0.00 2.29
2523 3959 3.580895 GCCTTGGGTCCCTTAAATTTTCA 59.419 43.478 10.00 0.00 0.00 2.69
2524 3960 4.225042 GCCTTGGGTCCCTTAAATTTTCAT 59.775 41.667 10.00 0.00 0.00 2.57
2525 3961 5.423931 GCCTTGGGTCCCTTAAATTTTCATA 59.576 40.000 10.00 0.00 0.00 2.15
2526 3962 6.406961 GCCTTGGGTCCCTTAAATTTTCATAG 60.407 42.308 10.00 0.00 0.00 2.23
2527 3963 6.895204 CCTTGGGTCCCTTAAATTTTCATAGA 59.105 38.462 10.00 0.00 0.00 1.98
2528 3964 7.398904 CCTTGGGTCCCTTAAATTTTCATAGAA 59.601 37.037 10.00 0.00 0.00 2.10
2529 3965 8.728596 TTGGGTCCCTTAAATTTTCATAGAAA 57.271 30.769 10.00 0.00 0.00 2.52
2530 3966 8.728596 TGGGTCCCTTAAATTTTCATAGAAAA 57.271 30.769 10.00 7.30 0.00 2.29
2531 3967 9.332713 TGGGTCCCTTAAATTTTCATAGAAAAT 57.667 29.630 10.00 10.92 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.689347 TGGGTGAAACATTCTCCTCATG 58.311 45.455 10.11 0.00 41.78 3.07
1 2 4.018141 TCATGGGTGAAACATTCTCCTCAT 60.018 41.667 10.11 9.05 41.78 2.90
2 3 3.330405 TCATGGGTGAAACATTCTCCTCA 59.670 43.478 10.11 7.57 41.78 3.86
3 4 3.944015 CTCATGGGTGAAACATTCTCCTC 59.056 47.826 10.11 3.25 41.78 3.71
4 5 3.308688 CCTCATGGGTGAAACATTCTCCT 60.309 47.826 10.11 0.00 41.78 3.69
60 61 7.712639 TGATGTCTAAATCATAGACTTTGGAGC 59.287 37.037 14.64 0.85 43.15 4.70
83 88 9.192642 TGATATTTGACTTGTGAATTCCATGAT 57.807 29.630 2.27 0.00 0.00 2.45
84 89 8.578448 TGATATTTGACTTGTGAATTCCATGA 57.422 30.769 2.27 0.00 0.00 3.07
140 154 5.669798 ATCTACTTGGCCCCTTTGAATAT 57.330 39.130 0.00 0.00 0.00 1.28
205 219 7.389232 TCTATGCATGGATGTAATAAGTCCAG 58.611 38.462 8.93 0.00 44.59 3.86
206 220 7.315066 TCTATGCATGGATGTAATAAGTCCA 57.685 36.000 8.93 0.00 45.37 4.02
207 221 7.661437 TGTTCTATGCATGGATGTAATAAGTCC 59.339 37.037 14.04 0.00 0.00 3.85
209 223 8.213679 AGTGTTCTATGCATGGATGTAATAAGT 58.786 33.333 14.04 0.00 0.00 2.24
210 224 8.613060 AGTGTTCTATGCATGGATGTAATAAG 57.387 34.615 14.04 0.00 0.00 1.73
241 997 3.188492 CTGTTGCAGCATGTCTAGAGAG 58.812 50.000 2.87 0.00 39.31 3.20
442 1365 4.798574 CATTTTTCCTGCAGGTAAGACAC 58.201 43.478 31.58 0.00 36.34 3.67
612 1636 2.143925 CCCAAAGGAACTCTGTTCGAC 58.856 52.381 4.65 0.00 38.49 4.20
836 1881 6.387465 AGATCTTTGTCATGCATTCAACAAG 58.613 36.000 15.01 10.72 33.54 3.16
914 1964 9.250246 AGACATATCTAAAGCTAGATACTTCCC 57.750 37.037 8.13 0.00 45.65 3.97
1035 2087 5.632764 GTCATACTCAATCAGACCATCATCG 59.367 44.000 0.00 0.00 0.00 3.84
1047 2099 7.440198 TCTTGATCCTCATGTCATACTCAATC 58.560 38.462 0.00 0.00 0.00 2.67
1152 2204 5.065218 GTCGCCAGAGATGTTAAATGTGAAT 59.935 40.000 0.00 0.00 0.00 2.57
1181 2233 1.740296 GTTATGGCGACTGCACCGT 60.740 57.895 0.00 0.00 45.35 4.83
1240 2292 5.925397 CGCTCTGCACTTCTAATATGAGAAT 59.075 40.000 2.79 0.00 34.95 2.40
1250 2302 1.337823 GGAAACCGCTCTGCACTTCTA 60.338 52.381 0.00 0.00 0.00 2.10
1277 2329 4.003648 CCCACTGGTAAAACATCTGAGAC 58.996 47.826 0.00 0.00 0.00 3.36
1386 2438 8.830580 CATATCTTGAACTTCAAACGTATGGAT 58.169 33.333 5.72 5.78 35.73 3.41
1401 2453 6.565435 CGGATGATTCTGTGCATATCTTGAAC 60.565 42.308 0.00 0.00 34.02 3.18
1408 2460 4.511527 GATCCGGATGATTCTGTGCATAT 58.488 43.478 24.82 0.00 32.41 1.78
1417 2469 2.610727 GGAACTCGGATCCGGATGATTC 60.611 54.545 32.79 24.66 40.25 2.52
1418 2470 1.344763 GGAACTCGGATCCGGATGATT 59.655 52.381 32.79 19.14 40.25 2.57
1436 2488 0.038892 GAAGGTACAACGACGCTGGA 60.039 55.000 2.97 0.00 0.00 3.86
1440 2492 0.788391 CCTTGAAGGTACAACGACGC 59.212 55.000 2.25 0.00 0.00 5.19
1467 2519 2.101415 CTCTCGAGTGTTATGCCCATGA 59.899 50.000 13.13 0.00 0.00 3.07
1539 2600 1.869767 GAAAGCTACCAGGCATCATCG 59.130 52.381 0.00 0.00 34.17 3.84
1541 2602 1.849039 AGGAAAGCTACCAGGCATCAT 59.151 47.619 11.59 0.00 34.17 2.45
1566 2627 1.794701 GTTTACGGTCGGACAAACCTC 59.205 52.381 10.76 0.00 34.45 3.85
1620 2683 1.826720 TCCGGTCTGCCTAAATACGTT 59.173 47.619 0.00 0.00 0.00 3.99
1626 2689 0.896940 ACGACTCCGGTCTGCCTAAA 60.897 55.000 0.00 0.00 40.10 1.85
1693 2757 1.137513 GCGCTGGACCGAATATGTAC 58.862 55.000 0.00 0.00 0.00 2.90
1734 2798 4.779475 ACGGCAAGACTGTGGAAG 57.221 55.556 0.00 0.00 36.16 3.46
1739 2803 1.524961 TGGAACACGGCAAGACTGT 59.475 52.632 0.00 0.00 38.94 3.55
1740 2804 4.454948 TGGAACACGGCAAGACTG 57.545 55.556 0.00 0.00 0.00 3.51
1778 2842 2.969628 AATCCGTGTTGCCAAAACAA 57.030 40.000 0.00 0.00 31.20 2.83
1807 2871 3.059097 AGCTGGGAAATATCCTCCATGT 58.941 45.455 6.23 0.00 45.77 3.21
1808 2872 3.803186 AGCTGGGAAATATCCTCCATG 57.197 47.619 6.23 0.00 45.77 3.66
1836 2901 1.003355 ACCGTGAAGCCATCCTGTG 60.003 57.895 0.00 0.00 0.00 3.66
1837 2902 1.003355 CACCGTGAAGCCATCCTGT 60.003 57.895 0.00 0.00 0.00 4.00
1838 2903 2.401766 GCACCGTGAAGCCATCCTG 61.402 63.158 1.65 0.00 0.00 3.86
1839 2904 2.045926 GCACCGTGAAGCCATCCT 60.046 61.111 1.65 0.00 0.00 3.24
1840 2905 1.750399 ATGCACCGTGAAGCCATCC 60.750 57.895 1.65 0.00 0.00 3.51
1841 2906 1.026182 TCATGCACCGTGAAGCCATC 61.026 55.000 1.65 0.00 0.00 3.51
1842 2907 1.002257 TCATGCACCGTGAAGCCAT 60.002 52.632 1.65 0.00 0.00 4.40
1843 2908 1.672030 CTCATGCACCGTGAAGCCA 60.672 57.895 1.65 0.00 0.00 4.75
1844 2909 0.955428 TTCTCATGCACCGTGAAGCC 60.955 55.000 1.65 0.00 0.00 4.35
1845 2910 0.445436 CTTCTCATGCACCGTGAAGC 59.555 55.000 13.68 0.00 30.06 3.86
1846 2911 2.084610 TCTTCTCATGCACCGTGAAG 57.915 50.000 17.54 17.54 36.03 3.02
1847 2912 2.542020 TTCTTCTCATGCACCGTGAA 57.458 45.000 1.65 0.00 0.00 3.18
1848 2913 2.743664 CAATTCTTCTCATGCACCGTGA 59.256 45.455 1.65 0.00 0.00 4.35
1849 2914 2.159476 CCAATTCTTCTCATGCACCGTG 60.159 50.000 0.00 0.00 0.00 4.94
1850 2915 2.086869 CCAATTCTTCTCATGCACCGT 58.913 47.619 0.00 0.00 0.00 4.83
1851 2916 2.358957 TCCAATTCTTCTCATGCACCG 58.641 47.619 0.00 0.00 0.00 4.94
1852 2917 4.789012 TTTCCAATTCTTCTCATGCACC 57.211 40.909 0.00 0.00 0.00 5.01
1853 2918 6.869913 TCATTTTTCCAATTCTTCTCATGCAC 59.130 34.615 0.00 0.00 0.00 4.57
1854 2919 6.995364 TCATTTTTCCAATTCTTCTCATGCA 58.005 32.000 0.00 0.00 0.00 3.96
1855 2920 7.318141 TCTCATTTTTCCAATTCTTCTCATGC 58.682 34.615 0.00 0.00 0.00 4.06
1856 2921 8.521176 ACTCTCATTTTTCCAATTCTTCTCATG 58.479 33.333 0.00 0.00 0.00 3.07
1857 2922 8.521176 CACTCTCATTTTTCCAATTCTTCTCAT 58.479 33.333 0.00 0.00 0.00 2.90
1858 2923 7.720957 TCACTCTCATTTTTCCAATTCTTCTCA 59.279 33.333 0.00 0.00 0.00 3.27
1859 2924 8.103948 TCACTCTCATTTTTCCAATTCTTCTC 57.896 34.615 0.00 0.00 0.00 2.87
1860 2925 8.355913 GTTCACTCTCATTTTTCCAATTCTTCT 58.644 33.333 0.00 0.00 0.00 2.85
1861 2926 7.324616 CGTTCACTCTCATTTTTCCAATTCTTC 59.675 37.037 0.00 0.00 0.00 2.87
1862 2927 7.013274 TCGTTCACTCTCATTTTTCCAATTCTT 59.987 33.333 0.00 0.00 0.00 2.52
1863 2928 6.486657 TCGTTCACTCTCATTTTTCCAATTCT 59.513 34.615 0.00 0.00 0.00 2.40
1864 2929 6.668323 TCGTTCACTCTCATTTTTCCAATTC 58.332 36.000 0.00 0.00 0.00 2.17
1865 2930 6.633500 TCGTTCACTCTCATTTTTCCAATT 57.367 33.333 0.00 0.00 0.00 2.32
1866 2931 6.207417 ACATCGTTCACTCTCATTTTTCCAAT 59.793 34.615 0.00 0.00 0.00 3.16
1867 2932 5.530915 ACATCGTTCACTCTCATTTTTCCAA 59.469 36.000 0.00 0.00 0.00 3.53
1868 2933 5.063204 ACATCGTTCACTCTCATTTTTCCA 58.937 37.500 0.00 0.00 0.00 3.53
1869 2934 5.613358 ACATCGTTCACTCTCATTTTTCC 57.387 39.130 0.00 0.00 0.00 3.13
1870 2935 7.117241 TGTACATCGTTCACTCTCATTTTTC 57.883 36.000 0.00 0.00 0.00 2.29
1871 2936 7.387673 TCATGTACATCGTTCACTCTCATTTTT 59.612 33.333 5.07 0.00 0.00 1.94
1872 2937 6.873605 TCATGTACATCGTTCACTCTCATTTT 59.126 34.615 5.07 0.00 0.00 1.82
1873 2938 6.311445 GTCATGTACATCGTTCACTCTCATTT 59.689 38.462 5.07 0.00 0.00 2.32
1874 2939 5.807520 GTCATGTACATCGTTCACTCTCATT 59.192 40.000 5.07 0.00 0.00 2.57
1875 2940 5.126222 AGTCATGTACATCGTTCACTCTCAT 59.874 40.000 5.07 0.00 0.00 2.90
1876 2941 4.459337 AGTCATGTACATCGTTCACTCTCA 59.541 41.667 5.07 0.00 0.00 3.27
1895 2960 4.963318 AATCAGTCAGAAACAGGAGTCA 57.037 40.909 0.00 0.00 0.00 3.41
1937 3002 8.080417 GCACAGCATTCATAATGAATAGTTGAT 58.920 33.333 13.30 0.00 44.60 2.57
1962 3027 3.495001 GCTTCCATACCGAGTTTAGATGC 59.505 47.826 0.00 0.00 0.00 3.91
1974 3039 2.549754 CGTCATGAATGGCTTCCATACC 59.450 50.000 0.00 0.00 44.40 2.73
2001 3066 4.213482 ACTCGAGTCCAATTTTAACAGCAC 59.787 41.667 13.58 0.00 0.00 4.40
2072 3137 0.387112 AAATGCAATCACCACACGCG 60.387 50.000 3.53 3.53 0.00 6.01
2089 3155 3.273434 CATAGAGTGCAGCTAGGCAAAA 58.727 45.455 0.00 0.00 46.93 2.44
2155 3590 6.310224 GGTCTAAAACGCAACGTATTACCTAA 59.690 38.462 0.00 0.00 39.99 2.69
2166 3601 5.573669 TGAAACAAAAGGTCTAAAACGCAAC 59.426 36.000 0.00 0.00 0.00 4.17
2172 3607 6.887545 TCCTGAGTGAAACAAAAGGTCTAAAA 59.112 34.615 0.00 0.00 41.43 1.52
2238 3673 6.057321 TCCAAATACTCCGGTCTAAACATT 57.943 37.500 0.00 0.00 0.00 2.71
2246 3681 5.123227 TGATCATTTCCAAATACTCCGGTC 58.877 41.667 0.00 0.00 0.00 4.79
2286 3721 6.070194 AAGCTAGGATGTCCTAAAACTGCTTA 60.070 38.462 21.48 0.00 45.39 3.09
2329 3765 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2330 3766 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2331 3767 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2332 3768 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2333 3769 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2334 3770 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2335 3771 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2336 3772 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2340 3776 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2341 3777 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2342 3778 1.740025 CTAAGGCAGCAGCTTTACCAC 59.260 52.381 1.36 0.00 40.81 4.16
2343 3779 2.113860 CTAAGGCAGCAGCTTTACCA 57.886 50.000 1.36 0.00 40.81 3.25
2354 3790 1.303309 GGTGCATGTAGCTAAGGCAG 58.697 55.000 13.62 0.00 45.94 4.85
2355 3791 0.461870 CGGTGCATGTAGCTAAGGCA 60.462 55.000 11.25 10.24 45.94 4.75
2356 3792 1.160329 CCGGTGCATGTAGCTAAGGC 61.160 60.000 11.25 0.00 45.94 4.35
2357 3793 0.532862 CCCGGTGCATGTAGCTAAGG 60.533 60.000 11.25 5.09 45.94 2.69
2358 3794 1.160329 GCCCGGTGCATGTAGCTAAG 61.160 60.000 11.25 1.05 45.94 2.18
2359 3795 1.153249 GCCCGGTGCATGTAGCTAA 60.153 57.895 11.25 0.00 45.94 3.09
2360 3796 2.063979 AGCCCGGTGCATGTAGCTA 61.064 57.895 15.92 0.00 45.94 3.32
2361 3797 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
2362 3798 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
2363 3799 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
2364 3800 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
2377 3813 2.098770 GCATTTCTTCAAGCTAGGGCAG 59.901 50.000 0.00 0.00 41.70 4.85
2378 3814 2.094675 GCATTTCTTCAAGCTAGGGCA 58.905 47.619 0.00 0.00 41.70 5.36
2379 3815 2.094675 TGCATTTCTTCAAGCTAGGGC 58.905 47.619 0.00 0.00 39.06 5.19
2380 3816 3.084039 TGTGCATTTCTTCAAGCTAGGG 58.916 45.455 0.00 0.00 0.00 3.53
2381 3817 4.397103 TCATGTGCATTTCTTCAAGCTAGG 59.603 41.667 0.00 0.00 0.00 3.02
2382 3818 5.556355 TCATGTGCATTTCTTCAAGCTAG 57.444 39.130 0.00 0.00 0.00 3.42
2383 3819 5.416639 ACATCATGTGCATTTCTTCAAGCTA 59.583 36.000 0.00 0.00 0.00 3.32
2384 3820 4.219944 ACATCATGTGCATTTCTTCAAGCT 59.780 37.500 0.00 0.00 0.00 3.74
2385 3821 4.491676 ACATCATGTGCATTTCTTCAAGC 58.508 39.130 0.00 0.00 0.00 4.01
2386 3822 5.924254 ACAACATCATGTGCATTTCTTCAAG 59.076 36.000 0.00 0.00 30.82 3.02
2387 3823 5.845103 ACAACATCATGTGCATTTCTTCAA 58.155 33.333 0.00 0.00 30.82 2.69
2388 3824 5.456548 ACAACATCATGTGCATTTCTTCA 57.543 34.783 0.00 0.00 30.82 3.02
2389 3825 7.009815 CCAATACAACATCATGTGCATTTCTTC 59.990 37.037 0.00 0.00 34.75 2.87
2390 3826 6.814644 CCAATACAACATCATGTGCATTTCTT 59.185 34.615 0.00 0.00 34.75 2.52
2391 3827 6.071221 ACCAATACAACATCATGTGCATTTCT 60.071 34.615 0.00 0.00 34.75 2.52
2392 3828 6.035220 CACCAATACAACATCATGTGCATTTC 59.965 38.462 0.00 0.00 34.75 2.17
2393 3829 5.870433 CACCAATACAACATCATGTGCATTT 59.130 36.000 0.00 0.00 34.75 2.32
2394 3830 5.412640 CACCAATACAACATCATGTGCATT 58.587 37.500 0.00 0.00 34.75 3.56
2395 3831 4.142116 CCACCAATACAACATCATGTGCAT 60.142 41.667 0.00 0.00 34.75 3.96
2396 3832 3.193056 CCACCAATACAACATCATGTGCA 59.807 43.478 0.00 0.00 34.75 4.57
2397 3833 3.193267 ACCACCAATACAACATCATGTGC 59.807 43.478 0.00 0.00 34.75 4.57
2398 3834 5.048154 TGAACCACCAATACAACATCATGTG 60.048 40.000 0.00 0.00 34.75 3.21
2399 3835 5.076182 TGAACCACCAATACAACATCATGT 58.924 37.500 0.00 0.00 37.32 3.21
2400 3836 5.415389 TCTGAACCACCAATACAACATCATG 59.585 40.000 0.00 0.00 0.00 3.07
2401 3837 5.569355 TCTGAACCACCAATACAACATCAT 58.431 37.500 0.00 0.00 0.00 2.45
2402 3838 4.979335 TCTGAACCACCAATACAACATCA 58.021 39.130 0.00 0.00 0.00 3.07
2403 3839 6.324819 CAATCTGAACCACCAATACAACATC 58.675 40.000 0.00 0.00 0.00 3.06
2404 3840 5.185635 CCAATCTGAACCACCAATACAACAT 59.814 40.000 0.00 0.00 0.00 2.71
2405 3841 4.522405 CCAATCTGAACCACCAATACAACA 59.478 41.667 0.00 0.00 0.00 3.33
2406 3842 4.082245 CCCAATCTGAACCACCAATACAAC 60.082 45.833 0.00 0.00 0.00 3.32
2407 3843 4.085733 CCCAATCTGAACCACCAATACAA 58.914 43.478 0.00 0.00 0.00 2.41
2408 3844 3.696045 CCCAATCTGAACCACCAATACA 58.304 45.455 0.00 0.00 0.00 2.29
2409 3845 2.427095 GCCCAATCTGAACCACCAATAC 59.573 50.000 0.00 0.00 0.00 1.89
2410 3846 2.042297 TGCCCAATCTGAACCACCAATA 59.958 45.455 0.00 0.00 0.00 1.90
2411 3847 1.203162 TGCCCAATCTGAACCACCAAT 60.203 47.619 0.00 0.00 0.00 3.16
2412 3848 0.187117 TGCCCAATCTGAACCACCAA 59.813 50.000 0.00 0.00 0.00 3.67
2413 3849 0.539438 GTGCCCAATCTGAACCACCA 60.539 55.000 0.00 0.00 0.00 4.17
2414 3850 0.251341 AGTGCCCAATCTGAACCACC 60.251 55.000 0.00 0.00 0.00 4.61
2415 3851 1.168714 GAGTGCCCAATCTGAACCAC 58.831 55.000 0.00 0.00 0.00 4.16
2416 3852 0.038166 GGAGTGCCCAATCTGAACCA 59.962 55.000 0.00 0.00 34.14 3.67
2417 3853 2.873797 GGAGTGCCCAATCTGAACC 58.126 57.895 0.00 0.00 34.14 3.62
2428 3864 1.486211 TAGAGCAACTAGGGAGTGCC 58.514 55.000 0.00 0.00 35.52 5.01
2429 3865 3.257127 CCTATAGAGCAACTAGGGAGTGC 59.743 52.174 0.00 0.00 35.52 4.40
2430 3866 3.257127 GCCTATAGAGCAACTAGGGAGTG 59.743 52.174 0.00 0.00 35.52 3.51
2431 3867 3.502356 GCCTATAGAGCAACTAGGGAGT 58.498 50.000 0.00 0.00 37.59 3.85
2432 3868 2.829120 GGCCTATAGAGCAACTAGGGAG 59.171 54.545 0.00 4.75 34.35 4.30
2433 3869 2.179204 TGGCCTATAGAGCAACTAGGGA 59.821 50.000 3.32 0.00 34.35 4.20
2434 3870 2.609747 TGGCCTATAGAGCAACTAGGG 58.390 52.381 3.32 0.00 34.35 3.53
2435 3871 3.834813 TGATGGCCTATAGAGCAACTAGG 59.165 47.826 3.32 0.00 34.35 3.02
2436 3872 5.674052 ATGATGGCCTATAGAGCAACTAG 57.326 43.478 3.32 0.00 34.35 2.57
2437 3873 7.739995 ATAATGATGGCCTATAGAGCAACTA 57.260 36.000 3.32 0.00 35.42 2.24
2438 3874 4.989875 AATGATGGCCTATAGAGCAACT 57.010 40.909 3.32 0.00 0.00 3.16
2439 3875 7.278868 GTGTATAATGATGGCCTATAGAGCAAC 59.721 40.741 3.32 0.00 0.00 4.17
2440 3876 7.180946 AGTGTATAATGATGGCCTATAGAGCAA 59.819 37.037 3.32 0.00 0.00 3.91
2441 3877 6.669591 AGTGTATAATGATGGCCTATAGAGCA 59.330 38.462 3.32 0.00 0.00 4.26
2442 3878 6.983307 CAGTGTATAATGATGGCCTATAGAGC 59.017 42.308 3.32 2.99 0.00 4.09
2443 3879 8.298729 TCAGTGTATAATGATGGCCTATAGAG 57.701 38.462 3.32 0.00 0.00 2.43
2444 3880 7.343057 CCTCAGTGTATAATGATGGCCTATAGA 59.657 40.741 3.32 0.00 29.56 1.98
2445 3881 7.124901 ACCTCAGTGTATAATGATGGCCTATAG 59.875 40.741 3.32 0.00 29.56 1.31
2446 3882 6.959954 ACCTCAGTGTATAATGATGGCCTATA 59.040 38.462 3.32 0.00 29.56 1.31
2447 3883 5.787494 ACCTCAGTGTATAATGATGGCCTAT 59.213 40.000 3.32 0.00 29.56 2.57
2448 3884 5.155161 ACCTCAGTGTATAATGATGGCCTA 58.845 41.667 3.32 0.00 29.56 3.93
2449 3885 3.976654 ACCTCAGTGTATAATGATGGCCT 59.023 43.478 3.32 0.00 29.56 5.19
2450 3886 4.357918 ACCTCAGTGTATAATGATGGCC 57.642 45.455 0.00 0.00 29.56 5.36
2451 3887 5.368145 TGAACCTCAGTGTATAATGATGGC 58.632 41.667 0.00 0.00 29.56 4.40
2452 3888 5.994054 CCTGAACCTCAGTGTATAATGATGG 59.006 44.000 3.15 0.00 42.80 3.51
2453 3889 5.994054 CCCTGAACCTCAGTGTATAATGATG 59.006 44.000 3.15 0.00 42.80 3.07
2454 3890 5.455326 GCCCTGAACCTCAGTGTATAATGAT 60.455 44.000 3.15 0.00 42.80 2.45
2455 3891 4.141711 GCCCTGAACCTCAGTGTATAATGA 60.142 45.833 3.15 0.00 42.80 2.57
2456 3892 4.130118 GCCCTGAACCTCAGTGTATAATG 58.870 47.826 3.15 0.00 42.80 1.90
2457 3893 3.136626 GGCCCTGAACCTCAGTGTATAAT 59.863 47.826 0.00 0.00 42.80 1.28
2458 3894 2.504175 GGCCCTGAACCTCAGTGTATAA 59.496 50.000 0.00 0.00 42.80 0.98
2459 3895 2.116238 GGCCCTGAACCTCAGTGTATA 58.884 52.381 0.00 0.00 42.80 1.47
2460 3896 0.912486 GGCCCTGAACCTCAGTGTAT 59.088 55.000 0.00 0.00 42.80 2.29
2461 3897 0.178903 AGGCCCTGAACCTCAGTGTA 60.179 55.000 0.00 0.00 42.80 2.90
2462 3898 1.062488 AAGGCCCTGAACCTCAGTGT 61.062 55.000 0.00 0.00 42.80 3.55
2463 3899 0.111253 AAAGGCCCTGAACCTCAGTG 59.889 55.000 0.00 0.00 42.80 3.66
2464 3900 0.853530 AAAAGGCCCTGAACCTCAGT 59.146 50.000 0.00 0.00 42.80 3.41
2465 3901 1.251251 CAAAAGGCCCTGAACCTCAG 58.749 55.000 0.00 0.00 43.91 3.35
2466 3902 0.827507 GCAAAAGGCCCTGAACCTCA 60.828 55.000 0.00 0.00 36.14 3.86
2467 3903 0.540597 AGCAAAAGGCCCTGAACCTC 60.541 55.000 0.00 0.00 46.50 3.85
2468 3904 0.777446 TAGCAAAAGGCCCTGAACCT 59.223 50.000 0.00 0.00 46.50 3.50
2469 3905 1.627864 TTAGCAAAAGGCCCTGAACC 58.372 50.000 0.00 0.00 46.50 3.62
2470 3906 3.961480 ATTTAGCAAAAGGCCCTGAAC 57.039 42.857 0.00 0.00 46.50 3.18
2471 3907 5.542251 AGTTAATTTAGCAAAAGGCCCTGAA 59.458 36.000 0.00 0.00 46.50 3.02
2472 3908 5.083821 AGTTAATTTAGCAAAAGGCCCTGA 58.916 37.500 0.00 0.00 46.50 3.86
2473 3909 5.047377 TGAGTTAATTTAGCAAAAGGCCCTG 60.047 40.000 0.00 0.00 46.50 4.45
2474 3910 5.083821 TGAGTTAATTTAGCAAAAGGCCCT 58.916 37.500 0.00 0.00 46.50 5.19
2475 3911 5.400066 TGAGTTAATTTAGCAAAAGGCCC 57.600 39.130 0.00 0.00 46.50 5.80
2476 3912 5.047306 ACCTGAGTTAATTTAGCAAAAGGCC 60.047 40.000 0.00 0.00 46.50 5.19
2477 3913 5.863935 CACCTGAGTTAATTTAGCAAAAGGC 59.136 40.000 0.00 0.00 45.30 4.35
2478 3914 5.863935 GCACCTGAGTTAATTTAGCAAAAGG 59.136 40.000 0.00 0.00 0.00 3.11
2479 3915 5.863935 GGCACCTGAGTTAATTTAGCAAAAG 59.136 40.000 0.00 0.00 0.00 2.27
2480 3916 5.538433 AGGCACCTGAGTTAATTTAGCAAAA 59.462 36.000 0.00 0.00 0.00 2.44
2481 3917 5.076873 AGGCACCTGAGTTAATTTAGCAAA 58.923 37.500 0.00 0.00 0.00 3.68
2482 3918 4.662278 AGGCACCTGAGTTAATTTAGCAA 58.338 39.130 0.00 0.00 0.00 3.91
2483 3919 4.301072 AGGCACCTGAGTTAATTTAGCA 57.699 40.909 0.00 0.00 0.00 3.49
2484 3920 4.142381 CCAAGGCACCTGAGTTAATTTAGC 60.142 45.833 0.00 0.00 0.00 3.09
2485 3921 4.399303 CCCAAGGCACCTGAGTTAATTTAG 59.601 45.833 0.00 0.00 0.00 1.85
2486 3922 4.202631 ACCCAAGGCACCTGAGTTAATTTA 60.203 41.667 0.00 0.00 0.00 1.40
2487 3923 3.165071 CCCAAGGCACCTGAGTTAATTT 58.835 45.455 0.00 0.00 0.00 1.82
2488 3924 2.110011 ACCCAAGGCACCTGAGTTAATT 59.890 45.455 0.00 0.00 0.00 1.40
2489 3925 1.710809 ACCCAAGGCACCTGAGTTAAT 59.289 47.619 0.00 0.00 0.00 1.40
2490 3926 1.073284 GACCCAAGGCACCTGAGTTAA 59.927 52.381 0.00 0.00 0.00 2.01
2491 3927 0.690762 GACCCAAGGCACCTGAGTTA 59.309 55.000 0.00 0.00 0.00 2.24
2492 3928 1.456287 GACCCAAGGCACCTGAGTT 59.544 57.895 0.00 0.00 0.00 3.01
2493 3929 2.529744 GGACCCAAGGCACCTGAGT 61.530 63.158 0.00 0.00 0.00 3.41
2494 3930 2.352805 GGACCCAAGGCACCTGAG 59.647 66.667 0.00 0.00 0.00 3.35
2495 3931 3.256960 GGGACCCAAGGCACCTGA 61.257 66.667 5.33 0.00 0.00 3.86
2496 3932 1.497309 TAAGGGACCCAAGGCACCTG 61.497 60.000 14.60 0.00 33.38 4.00
2497 3933 0.774491 TTAAGGGACCCAAGGCACCT 60.774 55.000 14.60 0.00 34.29 4.00
2498 3934 0.113580 TTTAAGGGACCCAAGGCACC 59.886 55.000 14.60 0.00 0.00 5.01
2499 3935 2.231716 ATTTAAGGGACCCAAGGCAC 57.768 50.000 14.60 0.00 0.00 5.01
2500 3936 3.268034 AAATTTAAGGGACCCAAGGCA 57.732 42.857 14.60 0.00 0.00 4.75
2501 3937 3.580895 TGAAAATTTAAGGGACCCAAGGC 59.419 43.478 14.60 0.00 0.00 4.35
2502 3938 6.895204 TCTATGAAAATTTAAGGGACCCAAGG 59.105 38.462 14.60 0.00 0.00 3.61
2503 3939 7.954666 TCTATGAAAATTTAAGGGACCCAAG 57.045 36.000 14.60 0.00 0.00 3.61
2504 3940 8.728596 TTTCTATGAAAATTTAAGGGACCCAA 57.271 30.769 14.60 0.00 0.00 4.12
2505 3941 8.728596 TTTTCTATGAAAATTTAAGGGACCCA 57.271 30.769 14.60 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.