Multiple sequence alignment - TraesCS6D01G193200

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 TraesCS6D01G193200 chr6D 100.000 2703 0 0 1 2703 267516418 267513716 0.000000e+00 4992.0
1 TraesCS6D01G193200 chr6D 98.945 474 5 0 1229 1702 267237308 267236835 0.000000e+00 848.0
2 TraesCS6D01G193200 chr6D 96.629 178 5 1 1758 1935 10726284 10726108 7.320000e-76 294.0
3 TraesCS6D01G193200 chr6D 94.149 188 9 2 1743 1929 286634158 286634344 4.400000e-73 285.0
4 TraesCS6D01G193200 chr6D 92.593 135 10 0 1017 1151 267237713 267237579 7.640000e-46 195.0
5 TraesCS6D01G193200 chr6D 96.923 65 2 0 2639 2703 124791922 124791986 2.850000e-20 110.0
6 TraesCS6D01G193200 chr6A 93.552 1644 57 17 129 1738 381027251 381025623 0.000000e+00 2403.0
7 TraesCS6D01G193200 chr6A 96.680 512 16 1 1220 1730 380361718 380361207 0.000000e+00 850.0
8 TraesCS6D01G193200 chr6A 87.115 357 44 2 2263 2619 381025233 381024879 1.170000e-108 403.0
9 TraesCS6D01G193200 chr6A 88.646 229 17 5 1927 2150 381025575 381025351 1.230000e-68 270.0
10 TraesCS6D01G193200 chr6A 91.852 135 11 0 1017 1151 380362111 380361977 3.550000e-44 189.0
11 TraesCS6D01G193200 chr6B 92.290 1297 69 18 495 1768 415864903 415863615 0.000000e+00 1812.0
12 TraesCS6D01G193200 chr6B 98.734 474 6 0 1229 1702 415789546 415789073 0.000000e+00 843.0
13 TraesCS6D01G193200 chr6B 90.083 363 29 6 2259 2619 415863231 415862874 5.270000e-127 464.0
14 TraesCS6D01G193200 chr6B 82.241 473 32 24 16 445 415865375 415864912 7.110000e-96 361.0
15 TraesCS6D01G193200 chr6B 86.111 216 19 9 2007 2220 415863506 415863300 3.500000e-54 222.0
16 TraesCS6D01G193200 chr6B 92.593 135 10 0 1017 1151 415789910 415789776 7.640000e-46 195.0
17 TraesCS6D01G193200 chr5D 87.526 978 81 20 815 1768 531972123 531971163 0.000000e+00 1092.0
18 TraesCS6D01G193200 chr5D 86.555 476 42 12 1222 1679 531901308 531900837 3.110000e-139 505.0
19 TraesCS6D01G193200 chr5D 97.674 172 2 2 1766 1937 29505416 29505247 7.320000e-76 294.0
20 TraesCS6D01G193200 chr5D 97.143 175 4 1 1756 1930 74043518 74043345 7.320000e-76 294.0
21 TraesCS6D01G193200 chr5D 93.151 146 10 0 1013 1158 531902150 531902005 5.860000e-52 215.0
22 TraesCS6D01G193200 chr5D 95.775 71 2 1 2634 2703 162120438 162120368 2.200000e-21 113.0
23 TraesCS6D01G193200 chr5D 93.243 74 5 0 2630 2703 281823610 281823537 2.850000e-20 110.0
24 TraesCS6D01G193200 chr5D 100.000 29 0 0 2189 2217 320448942 320448914 1.000000e-03 54.7
25 TraesCS6D01G193200 chr4A 87.066 951 85 22 815 1752 640232204 640233129 0.000000e+00 1040.0
26 TraesCS6D01G193200 chr4A 93.878 49 1 2 304 351 640218868 640218915 3.730000e-09 73.1
27 TraesCS6D01G193200 chr5B 87.827 879 74 15 842 1706 671188521 671187662 0.000000e+00 1000.0
28 TraesCS6D01G193200 chr5B 85.470 351 34 10 815 1160 671138248 671137910 1.540000e-92 350.0
29 TraesCS6D01G193200 chr5B 85.567 291 42 0 1216 1506 671131630 671131340 3.380000e-79 305.0
30 TraesCS6D01G193200 chr5B 90.000 180 12 5 1503 1679 671131232 671131056 7.530000e-56 228.0
31 TraesCS6D01G193200 chr5B 96.970 66 1 1 2638 2703 62909721 62909785 2.850000e-20 110.0
32 TraesCS6D01G193200 chr4D 97.688 173 3 1 1757 1929 113186976 113187147 2.030000e-76 296.0
33 TraesCS6D01G193200 chr7D 97.159 176 2 3 1759 1933 134105091 134104918 7.320000e-76 294.0
34 TraesCS6D01G193200 chr3D 97.143 175 3 2 1765 1938 32278346 32278173 7.320000e-76 294.0
35 TraesCS6D01G193200 chr3D 97.126 174 3 2 1762 1935 500915073 500914902 2.630000e-75 292.0
36 TraesCS6D01G193200 chr3D 98.193 166 3 0 1765 1930 566956126 566956291 9.470000e-75 291.0
37 TraesCS6D01G193200 chr7B 96.923 65 2 0 2639 2703 282654414 282654478 2.850000e-20 110.0
38 TraesCS6D01G193200 chr3B 96.923 65 2 0 2639 2703 109514647 109514583 2.850000e-20 110.0
39 TraesCS6D01G193200 chr2D 96.970 66 1 1 2638 2703 289378892 289378956 2.850000e-20 110.0
40 TraesCS6D01G193200 chr2D 96.923 65 2 0 2639 2703 532031250 532031186 2.850000e-20 110.0
41 TraesCS6D01G193200 chr1D 96.923 65 2 0 2639 2703 260038974 260039038 2.850000e-20 110.0


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 TraesCS6D01G193200 chr6D 267513716 267516418 2702 True 4992.000000 4992 100.00000 1 2703 1 chr6D.!!$R2 2702
1 TraesCS6D01G193200 chr6D 267236835 267237713 878 True 521.500000 848 95.76900 1017 1702 2 chr6D.!!$R3 685
2 TraesCS6D01G193200 chr6A 381024879 381027251 2372 True 1025.333333 2403 89.77100 129 2619 3 chr6A.!!$R2 2490
3 TraesCS6D01G193200 chr6A 380361207 380362111 904 True 519.500000 850 94.26600 1017 1730 2 chr6A.!!$R1 713
4 TraesCS6D01G193200 chr6B 415862874 415865375 2501 True 714.750000 1812 87.68125 16 2619 4 chr6B.!!$R2 2603
5 TraesCS6D01G193200 chr6B 415789073 415789910 837 True 519.000000 843 95.66350 1017 1702 2 chr6B.!!$R1 685
6 TraesCS6D01G193200 chr5D 531971163 531972123 960 True 1092.000000 1092 87.52600 815 1768 1 chr5D.!!$R6 953
7 TraesCS6D01G193200 chr5D 531900837 531902150 1313 True 360.000000 505 89.85300 1013 1679 2 chr5D.!!$R7 666
8 TraesCS6D01G193200 chr4A 640232204 640233129 925 False 1040.000000 1040 87.06600 815 1752 1 chr4A.!!$F2 937
9 TraesCS6D01G193200 chr5B 671187662 671188521 859 True 1000.000000 1000 87.82700 842 1706 1 chr5B.!!$R2 864
10 TraesCS6D01G193200 chr5B 671131056 671131630 574 True 266.500000 305 87.78350 1216 1679 2 chr5B.!!$R3 463

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
729 781 0.106619 TCTTCCGGACCCTCTAGAGC 60.107 60.0 14.73 0.63 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 3395 0.321298 GCCTTGCGGGTCTCTGTTAA 60.321 55.0 0.0 0.0 37.43 2.01 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
42 43 3.906846 AGGGAGCCTAGATATGAAACCTG 59.093 47.826 0.00 0.00 28.47 4.00
43 44 3.648545 GGGAGCCTAGATATGAAACCTGT 59.351 47.826 0.00 0.00 0.00 4.00
45 46 5.279556 GGGAGCCTAGATATGAAACCTGTAC 60.280 48.000 0.00 0.00 0.00 2.90
51 52 7.520614 GCCTAGATATGAAACCTGTACAATTGC 60.521 40.741 5.05 0.00 0.00 3.56
52 53 7.716998 CCTAGATATGAAACCTGTACAATTGCT 59.283 37.037 5.05 0.00 0.00 3.91
66 74 9.814507 CTGTACAATTGCTAACGTTTTATACAA 57.185 29.630 5.91 4.92 0.00 2.41
82 90 6.925610 TTATACAATTCTTGCTGTGCTAGG 57.074 37.500 0.00 0.00 32.69 3.02
83 91 3.146104 ACAATTCTTGCTGTGCTAGGT 57.854 42.857 0.00 0.00 32.69 3.08
84 92 3.490348 ACAATTCTTGCTGTGCTAGGTT 58.510 40.909 0.00 0.00 32.69 3.50
119 127 1.987855 CACCGGTGGCTCCTCCTAA 60.988 63.158 27.57 0.00 35.26 2.69
121 129 2.494918 CGGTGGCTCCTCCTAACG 59.505 66.667 3.83 0.00 35.26 3.18
122 130 2.348888 CGGTGGCTCCTCCTAACGT 61.349 63.158 3.83 0.00 35.26 3.99
124 132 0.323957 GGTGGCTCCTCCTAACGTTT 59.676 55.000 5.91 0.00 35.26 3.60
126 134 2.027837 GGTGGCTCCTCCTAACGTTTTA 60.028 50.000 5.91 0.00 35.26 1.52
127 135 3.370209 GGTGGCTCCTCCTAACGTTTTAT 60.370 47.826 5.91 0.00 35.26 1.40
225 262 4.491676 GTTATGGCTAAGAGTCACGTGAA 58.508 43.478 21.95 2.84 29.65 3.18
266 309 5.212532 TCTTGTTGTATTGCAATGGCTTT 57.787 34.783 22.27 0.00 41.91 3.51
466 513 2.462456 TGCAGCTGTAGACAAGGAAG 57.538 50.000 16.64 0.00 0.00 3.46
470 517 2.497675 CAGCTGTAGACAAGGAAGGCTA 59.502 50.000 5.25 0.00 0.00 3.93
588 638 4.023963 ACGATGATACATGTACTCGACTGG 60.024 45.833 27.53 10.53 0.00 4.00
723 775 2.754658 TCGCTCTTCCGGACCCTC 60.755 66.667 1.83 0.00 0.00 4.30
725 777 1.453379 CGCTCTTCCGGACCCTCTA 60.453 63.158 1.83 0.00 0.00 2.43
729 781 0.106619 TCTTCCGGACCCTCTAGAGC 60.107 60.000 14.73 0.63 0.00 4.09
730 782 0.395862 CTTCCGGACCCTCTAGAGCA 60.396 60.000 14.73 0.00 0.00 4.26
731 783 0.261991 TTCCGGACCCTCTAGAGCAT 59.738 55.000 14.73 3.90 0.00 3.79
733 785 1.182385 CCGGACCCTCTAGAGCATCC 61.182 65.000 22.23 22.23 33.66 3.51
734 786 1.519751 CGGACCCTCTAGAGCATCCG 61.520 65.000 31.84 31.84 43.23 4.18
735 787 1.663173 GACCCTCTAGAGCATCCGC 59.337 63.158 14.73 0.00 33.66 5.54
901 988 4.986659 CCTACATATACACGCTAAACCCAC 59.013 45.833 0.00 0.00 0.00 4.61
910 997 0.459063 GCTAAACCCACCCGTACTCG 60.459 60.000 0.00 0.00 0.00 4.18
1181 1748 4.452825 TCTCACGGATTGGTGTTAACAAA 58.547 39.130 10.51 2.22 39.00 2.83
1227 2182 7.731556 TCTTCTTAACGCTAACGACTAAATC 57.268 36.000 0.00 0.00 43.93 2.17
1714 2798 5.272283 AGAACAACTAAACTCGGAAGTCA 57.728 39.130 0.00 0.00 33.48 3.41
1725 2809 2.027625 GGAAGTCAGAACCGTGGCG 61.028 63.158 0.00 0.00 0.00 5.69
1768 2864 3.188159 TCTTGTCCTTTGCAACGTACT 57.812 42.857 0.00 0.00 0.00 2.73
1770 2866 1.873698 TGTCCTTTGCAACGTACTCC 58.126 50.000 0.00 0.00 0.00 3.85
1771 2867 1.154197 GTCCTTTGCAACGTACTCCC 58.846 55.000 0.00 0.00 0.00 4.30
1772 2868 1.053424 TCCTTTGCAACGTACTCCCT 58.947 50.000 0.00 0.00 0.00 4.20
1773 2869 1.001633 TCCTTTGCAACGTACTCCCTC 59.998 52.381 0.00 0.00 0.00 4.30
1774 2870 1.439679 CTTTGCAACGTACTCCCTCC 58.560 55.000 0.00 0.00 0.00 4.30
1775 2871 0.320073 TTTGCAACGTACTCCCTCCG 60.320 55.000 0.00 0.00 0.00 4.63
1776 2872 1.466025 TTGCAACGTACTCCCTCCGT 61.466 55.000 0.00 0.00 36.17 4.69
1777 2873 1.291272 GCAACGTACTCCCTCCGTT 59.709 57.895 0.00 0.00 44.81 4.44
1778 2874 0.735287 GCAACGTACTCCCTCCGTTC 60.735 60.000 0.00 0.00 42.34 3.95
1779 2875 0.108945 CAACGTACTCCCTCCGTTCC 60.109 60.000 0.00 0.00 42.34 3.62
1780 2876 0.251519 AACGTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 40.46 3.36
1781 2877 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
1782 2878 1.004745 ACGTACTCCCTCCGTTCCTAA 59.995 52.381 0.00 0.00 0.00 2.69
1783 2879 2.094675 CGTACTCCCTCCGTTCCTAAA 58.905 52.381 0.00 0.00 0.00 1.85
1784 2880 2.692041 CGTACTCCCTCCGTTCCTAAAT 59.308 50.000 0.00 0.00 0.00 1.40
1785 2881 3.885297 CGTACTCCCTCCGTTCCTAAATA 59.115 47.826 0.00 0.00 0.00 1.40
1786 2882 4.261363 CGTACTCCCTCCGTTCCTAAATAC 60.261 50.000 0.00 0.00 0.00 1.89
1787 2883 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1788 2884 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1789 2885 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1790 2886 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1791 2887 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
1792 2888 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
1793 2889 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1794 2890 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
1795 2891 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
1796 2892 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
1797 2893 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
1798 2894 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
1799 2895 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
1800 2896 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
1801 2897 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
1802 2898 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
1803 2899 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
1804 2900 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
1806 2902 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
1807 2903 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
1808 2904 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
1809 2905 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
1810 2906 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
1811 2907 6.707440 TGTCTTTCTAGGCATTTCAACAAA 57.293 33.333 0.00 0.00 29.10 2.83
1812 2908 7.288810 TGTCTTTCTAGGCATTTCAACAAAT 57.711 32.000 0.00 0.00 29.10 2.32
1825 2921 7.915293 ATTTCAACAAATGACTACATACGGA 57.085 32.000 0.00 0.00 37.92 4.69
1826 2922 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
1827 2923 6.032956 TCAACAAATGACTACATACGGAGT 57.967 37.500 0.00 0.00 37.64 3.85
1828 2924 7.160547 TCAACAAATGACTACATACGGAGTA 57.839 36.000 0.00 0.00 39.62 2.59
1829 2925 7.604549 TCAACAAATGACTACATACGGAGTAA 58.395 34.615 0.00 0.00 39.00 2.24
1830 2926 8.089597 TCAACAAATGACTACATACGGAGTAAA 58.910 33.333 0.00 0.00 39.00 2.01
1845 2941 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
1846 2942 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
1876 2972 8.958119 AAATATGTCTACATACATCCGTTTGT 57.042 30.769 4.98 0.00 41.15 2.83
1877 2973 7.946655 ATATGTCTACATACATCCGTTTGTG 57.053 36.000 4.98 0.00 41.15 3.33
1878 2974 5.394224 TGTCTACATACATCCGTTTGTGA 57.606 39.130 0.00 0.00 37.77 3.58
1879 2975 5.972935 TGTCTACATACATCCGTTTGTGAT 58.027 37.500 0.00 0.00 37.77 3.06
1880 2976 7.102847 TGTCTACATACATCCGTTTGTGATA 57.897 36.000 0.00 0.00 37.77 2.15
1881 2977 7.200455 TGTCTACATACATCCGTTTGTGATAG 58.800 38.462 0.00 0.00 37.77 2.08
1882 2978 7.147966 TGTCTACATACATCCGTTTGTGATAGT 60.148 37.037 0.00 0.00 37.77 2.12
1883 2979 7.378995 GTCTACATACATCCGTTTGTGATAGTC 59.621 40.741 0.00 0.00 37.77 2.59
1884 2980 5.972935 ACATACATCCGTTTGTGATAGTCA 58.027 37.500 0.00 0.00 36.16 3.41
1885 2981 6.582636 ACATACATCCGTTTGTGATAGTCAT 58.417 36.000 0.00 0.00 36.16 3.06
1886 2982 7.047891 ACATACATCCGTTTGTGATAGTCATT 58.952 34.615 0.00 0.00 36.16 2.57
1887 2983 7.552687 ACATACATCCGTTTGTGATAGTCATTT 59.447 33.333 0.00 0.00 36.16 2.32
1888 2984 6.182039 ACATCCGTTTGTGATAGTCATTTG 57.818 37.500 0.00 0.00 0.00 2.32
1889 2985 5.937540 ACATCCGTTTGTGATAGTCATTTGA 59.062 36.000 0.00 0.00 0.00 2.69
1890 2986 6.429692 ACATCCGTTTGTGATAGTCATTTGAA 59.570 34.615 0.00 0.00 0.00 2.69
1891 2987 6.869315 TCCGTTTGTGATAGTCATTTGAAA 57.131 33.333 0.00 0.00 0.00 2.69
1892 2988 7.447374 TCCGTTTGTGATAGTCATTTGAAAT 57.553 32.000 0.00 0.00 0.00 2.17
1893 2989 7.304735 TCCGTTTGTGATAGTCATTTGAAATG 58.695 34.615 11.54 11.54 0.00 2.32
1894 2990 6.033831 CCGTTTGTGATAGTCATTTGAAATGC 59.966 38.462 12.86 8.33 0.00 3.56
1895 2991 6.033831 CGTTTGTGATAGTCATTTGAAATGCC 59.966 38.462 12.86 1.61 0.00 4.40
1896 2992 6.839124 TTGTGATAGTCATTTGAAATGCCT 57.161 33.333 12.86 9.73 0.00 4.75
1897 2993 7.936496 TTGTGATAGTCATTTGAAATGCCTA 57.064 32.000 10.59 10.59 0.00 3.93
1898 2994 7.558161 TGTGATAGTCATTTGAAATGCCTAG 57.442 36.000 13.20 0.00 0.00 3.02
1899 2995 7.337938 TGTGATAGTCATTTGAAATGCCTAGA 58.662 34.615 13.20 1.78 0.00 2.43
1900 2996 7.828717 TGTGATAGTCATTTGAAATGCCTAGAA 59.171 33.333 13.20 2.99 0.00 2.10
1901 2997 8.677300 GTGATAGTCATTTGAAATGCCTAGAAA 58.323 33.333 13.20 0.91 0.00 2.52
1902 2998 8.896744 TGATAGTCATTTGAAATGCCTAGAAAG 58.103 33.333 13.20 0.00 0.00 2.62
1903 2999 9.113838 GATAGTCATTTGAAATGCCTAGAAAGA 57.886 33.333 13.20 0.00 0.00 2.52
1904 3000 7.150783 AGTCATTTGAAATGCCTAGAAAGAC 57.849 36.000 12.86 3.23 0.00 3.01
1905 3001 6.716628 AGTCATTTGAAATGCCTAGAAAGACA 59.283 34.615 12.86 0.00 0.00 3.41
1906 3002 7.231317 AGTCATTTGAAATGCCTAGAAAGACAA 59.769 33.333 12.86 0.00 0.00 3.18
1907 3003 7.540055 GTCATTTGAAATGCCTAGAAAGACAAG 59.460 37.037 12.86 0.00 0.00 3.16
1908 3004 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
1909 3005 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
1910 3006 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
1911 3007 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
1912 3008 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
1913 3009 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
1915 3011 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
1916 3012 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
1917 3013 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
1918 3014 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
1919 3015 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
1920 3016 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
1921 3017 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
1922 3018 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
1923 3019 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
1924 3020 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
1925 3021 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1926 3022 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1927 3023 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
1928 3024 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
1929 3025 4.892345 AGTATTTAGGAACGGAGGGAGTAC 59.108 45.833 0.00 0.00 0.00 2.73
1930 3026 1.755179 TTAGGAACGGAGGGAGTACG 58.245 55.000 0.00 0.00 0.00 3.67
1931 3027 0.620556 TAGGAACGGAGGGAGTACGT 59.379 55.000 0.00 0.00 43.43 3.57
2042 3190 1.813513 CCACCGATGGGCATATCTTC 58.186 55.000 0.00 0.00 43.04 2.87
2050 3206 4.021104 CGATGGGCATATCTTCTAGGAACA 60.021 45.833 0.00 0.00 0.00 3.18
2080 3249 5.681543 GGACGAGTTCTTCACATTTGTTTTC 59.318 40.000 0.00 0.00 0.00 2.29
2081 3250 6.189677 ACGAGTTCTTCACATTTGTTTTCA 57.810 33.333 0.00 0.00 0.00 2.69
2082 3251 6.027749 ACGAGTTCTTCACATTTGTTTTCAC 58.972 36.000 0.00 0.00 0.00 3.18
2083 3252 6.027131 CGAGTTCTTCACATTTGTTTTCACA 58.973 36.000 0.00 0.00 0.00 3.58
2084 3253 6.692681 CGAGTTCTTCACATTTGTTTTCACAT 59.307 34.615 0.00 0.00 31.06 3.21
2085 3254 7.220683 CGAGTTCTTCACATTTGTTTTCACATT 59.779 33.333 0.00 0.00 31.06 2.71
2086 3255 8.776376 AGTTCTTCACATTTGTTTTCACATTT 57.224 26.923 0.00 0.00 31.06 2.32
2087 3256 9.218440 AGTTCTTCACATTTGTTTTCACATTTT 57.782 25.926 0.00 0.00 31.06 1.82
2131 3301 4.681074 TGGATCAAAAACCCTGAAAACC 57.319 40.909 0.00 0.00 0.00 3.27
2151 3321 5.560966 ACCAATACATAAACAAAGAGCCG 57.439 39.130 0.00 0.00 0.00 5.52
2177 3347 3.569194 TGTCTGGGTCAAGCAGTTTTA 57.431 42.857 0.00 0.00 0.00 1.52
2182 3352 6.127196 TGTCTGGGTCAAGCAGTTTTAATTTT 60.127 34.615 0.00 0.00 0.00 1.82
2220 3390 7.630242 TGCCATTTTCATTAGTTAAGAGAGG 57.370 36.000 0.00 0.00 0.00 3.69
2221 3391 7.402054 TGCCATTTTCATTAGTTAAGAGAGGA 58.598 34.615 0.00 0.00 0.00 3.71
2222 3392 7.888021 TGCCATTTTCATTAGTTAAGAGAGGAA 59.112 33.333 0.00 0.00 0.00 3.36
2223 3393 8.907885 GCCATTTTCATTAGTTAAGAGAGGAAT 58.092 33.333 0.00 0.00 0.00 3.01
2240 3410 3.078837 GGAATTTTAACAGAGACCCGCA 58.921 45.455 0.00 0.00 0.00 5.69
2257 3433 1.977293 GCAAGGCGGGGAGAAGAGAT 61.977 60.000 0.00 0.00 0.00 2.75
2258 3434 1.414158 CAAGGCGGGGAGAAGAGATA 58.586 55.000 0.00 0.00 0.00 1.98
2259 3435 1.762957 CAAGGCGGGGAGAAGAGATAA 59.237 52.381 0.00 0.00 0.00 1.75
2260 3436 1.710816 AGGCGGGGAGAAGAGATAAG 58.289 55.000 0.00 0.00 0.00 1.73
2261 3437 1.062810 AGGCGGGGAGAAGAGATAAGT 60.063 52.381 0.00 0.00 0.00 2.24
2262 3438 1.069358 GGCGGGGAGAAGAGATAAGTG 59.931 57.143 0.00 0.00 0.00 3.16
2263 3439 1.539280 GCGGGGAGAAGAGATAAGTGC 60.539 57.143 0.00 0.00 0.00 4.40
2265 3441 1.418264 GGGGAGAAGAGATAAGTGCCC 59.582 57.143 0.00 0.00 0.00 5.36
2266 3442 2.119495 GGGAGAAGAGATAAGTGCCCA 58.881 52.381 0.00 0.00 34.47 5.36
2267 3443 2.708325 GGGAGAAGAGATAAGTGCCCAT 59.292 50.000 0.00 0.00 34.47 4.00
2316 3535 0.250510 TAACAATGGTCGCAGTGGCA 60.251 50.000 0.00 0.00 41.24 4.92
2371 3590 2.276732 TCAAAGCTCCCAGGAAACAG 57.723 50.000 0.00 0.00 0.00 3.16
2372 3591 1.774254 TCAAAGCTCCCAGGAAACAGA 59.226 47.619 0.00 0.00 0.00 3.41
2383 3602 2.620115 CAGGAAACAGACATGCACAAGT 59.380 45.455 0.00 0.00 0.00 3.16
2385 3604 4.275689 CAGGAAACAGACATGCACAAGTAA 59.724 41.667 0.00 0.00 0.00 2.24
2466 3685 2.746277 GACCTCGTGCCGCCAATT 60.746 61.111 0.00 0.00 0.00 2.32
2535 3754 2.802667 CGCGTTGGGAGAATCTGCG 61.803 63.158 0.00 0.00 38.04 5.18
2569 3788 2.677836 GTGAGGCGCAGATTCATTAACA 59.322 45.455 10.83 0.00 0.00 2.41
2621 3840 2.753029 AGCCCTGCTGTTCCACTC 59.247 61.111 0.00 0.00 37.57 3.51
2622 3841 2.360475 GCCCTGCTGTTCCACTCC 60.360 66.667 0.00 0.00 0.00 3.85
2623 3842 3.160585 CCCTGCTGTTCCACTCCA 58.839 61.111 0.00 0.00 0.00 3.86
2624 3843 1.455849 CCCTGCTGTTCCACTCCAA 59.544 57.895 0.00 0.00 0.00 3.53
2625 3844 0.178992 CCCTGCTGTTCCACTCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2626 3845 1.691196 CCTGCTGTTCCACTCCAAAA 58.309 50.000 0.00 0.00 0.00 2.44
2627 3846 2.242043 CCTGCTGTTCCACTCCAAAAT 58.758 47.619 0.00 0.00 0.00 1.82
2628 3847 2.629617 CCTGCTGTTCCACTCCAAAATT 59.370 45.455 0.00 0.00 0.00 1.82
2629 3848 3.553508 CCTGCTGTTCCACTCCAAAATTG 60.554 47.826 0.00 0.00 0.00 2.32
2660 3879 3.518992 AAAAACGATTCTTCCCCCTGA 57.481 42.857 0.00 0.00 0.00 3.86
2661 3880 2.491675 AAACGATTCTTCCCCCTGAC 57.508 50.000 0.00 0.00 0.00 3.51
2662 3881 1.358152 AACGATTCTTCCCCCTGACA 58.642 50.000 0.00 0.00 0.00 3.58
2663 3882 0.905357 ACGATTCTTCCCCCTGACAG 59.095 55.000 0.00 0.00 0.00 3.51
2664 3883 0.462759 CGATTCTTCCCCCTGACAGC 60.463 60.000 0.00 0.00 0.00 4.40
2665 3884 0.915364 GATTCTTCCCCCTGACAGCT 59.085 55.000 0.00 0.00 0.00 4.24
2666 3885 0.622665 ATTCTTCCCCCTGACAGCTG 59.377 55.000 13.48 13.48 0.00 4.24
2667 3886 1.492133 TTCTTCCCCCTGACAGCTGG 61.492 60.000 19.93 0.00 0.00 4.85
2673 3892 2.930019 CCTGACAGCTGGGACCCA 60.930 66.667 19.93 14.08 0.00 4.51
2674 3893 2.348998 CTGACAGCTGGGACCCAC 59.651 66.667 19.93 7.07 0.00 4.61
2675 3894 3.249189 TGACAGCTGGGACCCACC 61.249 66.667 19.93 2.66 38.08 4.61
2676 3895 3.249189 GACAGCTGGGACCCACCA 61.249 66.667 19.93 0.00 41.20 4.17
2683 3902 3.990492 TGGGACCCACCAGCTATAT 57.010 52.632 9.95 0.00 41.20 0.86
2684 3903 1.729586 TGGGACCCACCAGCTATATC 58.270 55.000 9.95 0.00 41.20 1.63
2685 3904 1.223077 TGGGACCCACCAGCTATATCT 59.777 52.381 9.95 0.00 41.20 1.98
2686 3905 2.339769 GGGACCCACCAGCTATATCTT 58.660 52.381 5.33 0.00 41.20 2.40
2687 3906 2.303311 GGGACCCACCAGCTATATCTTC 59.697 54.545 5.33 0.00 41.20 2.87
2688 3907 2.972713 GGACCCACCAGCTATATCTTCA 59.027 50.000 0.00 0.00 38.79 3.02
2689 3908 3.244249 GGACCCACCAGCTATATCTTCAC 60.244 52.174 0.00 0.00 38.79 3.18
2690 3909 3.384168 ACCCACCAGCTATATCTTCACA 58.616 45.455 0.00 0.00 0.00 3.58
2691 3910 3.134804 ACCCACCAGCTATATCTTCACAC 59.865 47.826 0.00 0.00 0.00 3.82
2692 3911 3.384668 CCACCAGCTATATCTTCACACG 58.615 50.000 0.00 0.00 0.00 4.49
2693 3912 3.384668 CACCAGCTATATCTTCACACGG 58.615 50.000 0.00 0.00 0.00 4.94
2694 3913 3.068165 CACCAGCTATATCTTCACACGGA 59.932 47.826 0.00 0.00 0.00 4.69
2695 3914 3.704566 ACCAGCTATATCTTCACACGGAA 59.295 43.478 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.883888 TAGGCTCCCTTTGGAACAATGC 60.884 50.000 0.00 0.00 41.17 3.56
9 10 3.019564 CTAGGCTCCCTTTGGAACAATG 58.980 50.000 0.00 0.00 41.17 2.82
10 11 2.919602 TCTAGGCTCCCTTTGGAACAAT 59.080 45.455 0.00 0.00 41.17 2.71
11 12 2.344592 TCTAGGCTCCCTTTGGAACAA 58.655 47.619 0.00 0.00 41.17 2.83
12 13 2.038863 TCTAGGCTCCCTTTGGAACA 57.961 50.000 0.00 0.00 41.17 3.18
13 14 4.348168 TCATATCTAGGCTCCCTTTGGAAC 59.652 45.833 0.00 0.00 41.17 3.62
14 15 4.566837 TCATATCTAGGCTCCCTTTGGAA 58.433 43.478 0.00 0.00 41.17 3.53
66 74 3.146104 ACAACCTAGCACAGCAAGAAT 57.854 42.857 0.00 0.00 0.00 2.40
82 90 4.418392 GGTGCAGATGAATCATCAACAAC 58.582 43.478 23.41 18.68 42.72 3.32
83 91 3.127376 CGGTGCAGATGAATCATCAACAA 59.873 43.478 23.41 5.14 42.72 2.83
84 92 2.679336 CGGTGCAGATGAATCATCAACA 59.321 45.455 23.41 17.46 42.72 3.33
119 127 6.569179 AGCCATTTGACTTGTATAAAACGT 57.431 33.333 0.00 0.00 0.00 3.99
121 129 8.515414 AGAGAAGCCATTTGACTTGTATAAAAC 58.485 33.333 0.00 0.00 0.00 2.43
122 130 8.635765 AGAGAAGCCATTTGACTTGTATAAAA 57.364 30.769 0.00 0.00 0.00 1.52
124 132 9.162764 GTAAGAGAAGCCATTTGACTTGTATAA 57.837 33.333 0.00 0.00 0.00 0.98
126 134 6.313905 CGTAAGAGAAGCCATTTGACTTGTAT 59.686 38.462 0.00 0.00 43.02 2.29
127 135 5.637810 CGTAAGAGAAGCCATTTGACTTGTA 59.362 40.000 0.00 0.00 43.02 2.41
225 262 2.158445 AGAGGTCCGAGGCATACATAGT 60.158 50.000 0.00 0.00 0.00 2.12
266 309 4.283678 CGACATTGAAAACGGCAGTTAAA 58.716 39.130 1.70 0.00 40.18 1.52
278 321 3.247173 GCAAAAACATGCCGACATTGAAA 59.753 39.130 0.00 0.00 40.49 2.69
279 322 2.799412 GCAAAAACATGCCGACATTGAA 59.201 40.909 0.00 0.00 40.49 2.69
397 440 6.857451 GCTGTTGCAAATTTTATCCCAAAAAG 59.143 34.615 0.00 0.00 39.41 2.27
466 513 3.274288 AGCATTTCTAGTGCAGTTAGCC 58.726 45.455 0.00 0.00 44.87 3.93
470 517 3.604582 GGAGAGCATTTCTAGTGCAGTT 58.395 45.455 0.00 0.00 44.87 3.16
588 638 4.388378 ACAAGAACTATTAGCTCGTCCC 57.612 45.455 0.00 0.00 0.00 4.46
729 781 4.161295 TTCTCCGGCCAGCGGATG 62.161 66.667 2.24 0.00 34.76 3.51
730 782 3.854669 CTTCTCCGGCCAGCGGAT 61.855 66.667 2.24 0.00 34.76 4.18
733 785 3.589654 TTGTCTTCTCCGGCCAGCG 62.590 63.158 2.24 0.00 0.00 5.18
734 786 0.889186 TTTTGTCTTCTCCGGCCAGC 60.889 55.000 2.24 0.00 0.00 4.85
735 787 1.826385 ATTTTGTCTTCTCCGGCCAG 58.174 50.000 2.24 0.00 0.00 4.85
736 788 3.426787 TTATTTTGTCTTCTCCGGCCA 57.573 42.857 2.24 0.00 0.00 5.36
768 838 5.051841 CGATCGAAAGTCAGATCATCAACTG 60.052 44.000 10.26 0.00 42.36 3.16
830 913 2.270205 CTGCCATCCCTCTTGCGT 59.730 61.111 0.00 0.00 0.00 5.24
901 988 0.945813 GAGAGATGGACGAGTACGGG 59.054 60.000 0.00 0.00 44.46 5.28
910 997 2.333069 TGATGGATGGGAGAGATGGAC 58.667 52.381 0.00 0.00 0.00 4.02
1181 1748 2.698797 TCCTTGTTTCCGTTCTCTGTCT 59.301 45.455 0.00 0.00 0.00 3.41
1321 2276 3.326747 GCTCACCTTCACGTTCTTGTAT 58.673 45.455 0.00 0.00 0.00 2.29
1714 2798 0.949105 GAACACATCGCCACGGTTCT 60.949 55.000 0.00 0.00 35.99 3.01
1725 2809 1.130613 GCGCACAGACGAACACATC 59.869 57.895 0.30 0.00 34.06 3.06
1737 2827 3.625232 GACAAGAAGTCGCGCACA 58.375 55.556 8.75 0.00 37.53 4.57
1768 2864 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1770 2866 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
1771 2867 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
1772 2868 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
1773 2869 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
1774 2870 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
1775 2871 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
1776 2872 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
1777 2873 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
1778 2874 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
1780 2876 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
1781 2877 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
1782 2878 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
1783 2879 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
1784 2880 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
1785 2881 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
1786 2882 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
1787 2883 6.707440 TTGTTGAAATGCCTAGAAAGACAA 57.293 33.333 0.00 0.00 0.00 3.18
1788 2884 6.707440 TTTGTTGAAATGCCTAGAAAGACA 57.293 33.333 0.00 0.00 0.00 3.41
1789 2885 7.327032 GTCATTTGTTGAAATGCCTAGAAAGAC 59.673 37.037 0.00 0.00 45.61 3.01
1790 2886 7.231317 AGTCATTTGTTGAAATGCCTAGAAAGA 59.769 33.333 0.00 0.00 45.61 2.52
1791 2887 7.373493 AGTCATTTGTTGAAATGCCTAGAAAG 58.627 34.615 0.00 0.00 45.61 2.62
1792 2888 7.288810 AGTCATTTGTTGAAATGCCTAGAAA 57.711 32.000 0.00 0.00 45.61 2.52
1793 2889 6.899393 AGTCATTTGTTGAAATGCCTAGAA 57.101 33.333 0.00 0.00 45.61 2.10
1794 2890 6.939730 TGTAGTCATTTGTTGAAATGCCTAGA 59.060 34.615 0.00 0.00 45.61 2.43
1795 2891 7.144722 TGTAGTCATTTGTTGAAATGCCTAG 57.855 36.000 0.00 0.00 45.61 3.02
1796 2892 7.701539 ATGTAGTCATTTGTTGAAATGCCTA 57.298 32.000 0.00 0.00 45.61 3.93
1797 2893 6.594788 ATGTAGTCATTTGTTGAAATGCCT 57.405 33.333 0.00 0.00 45.61 4.75
1798 2894 6.468956 CGTATGTAGTCATTTGTTGAAATGCC 59.531 38.462 0.00 0.00 45.61 4.40
1799 2895 6.468956 CCGTATGTAGTCATTTGTTGAAATGC 59.531 38.462 0.00 0.00 45.61 3.56
1800 2896 7.747888 TCCGTATGTAGTCATTTGTTGAAATG 58.252 34.615 0.00 0.00 46.84 2.32
1801 2897 7.606456 ACTCCGTATGTAGTCATTTGTTGAAAT 59.394 33.333 0.00 0.00 35.70 2.17
1802 2898 6.932400 ACTCCGTATGTAGTCATTTGTTGAAA 59.068 34.615 0.00 0.00 35.70 2.69
1803 2899 6.460781 ACTCCGTATGTAGTCATTTGTTGAA 58.539 36.000 0.00 0.00 35.70 2.69
1804 2900 6.032956 ACTCCGTATGTAGTCATTTGTTGA 57.967 37.500 0.00 0.00 35.70 3.18
1805 2901 7.821595 TTACTCCGTATGTAGTCATTTGTTG 57.178 36.000 0.00 0.00 35.70 3.33
1806 2902 8.836268 TTTTACTCCGTATGTAGTCATTTGTT 57.164 30.769 0.00 0.00 35.70 2.83
1807 2903 8.879759 CATTTTACTCCGTATGTAGTCATTTGT 58.120 33.333 0.00 0.00 35.70 2.83
1808 2904 9.093970 TCATTTTACTCCGTATGTAGTCATTTG 57.906 33.333 0.00 0.00 35.70 2.32
1809 2905 9.314321 CTCATTTTACTCCGTATGTAGTCATTT 57.686 33.333 0.00 0.00 35.70 2.32
1810 2906 8.475639 ACTCATTTTACTCCGTATGTAGTCATT 58.524 33.333 0.00 0.00 35.70 2.57
1811 2907 7.921214 CACTCATTTTACTCCGTATGTAGTCAT 59.079 37.037 0.00 0.00 38.00 3.06
1812 2908 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
1813 2909 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
1814 2910 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
1815 2911 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
1816 2912 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
1817 2913 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
1818 2914 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
1819 2915 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
1820 2916 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
1821 2917 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
1822 2918 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
1850 2946 9.391006 ACAAACGGATGTATGTAGACATATTTT 57.609 29.630 5.69 0.00 40.18 1.82
1851 2947 8.826710 CACAAACGGATGTATGTAGACATATTT 58.173 33.333 5.69 0.00 40.18 1.40
1852 2948 8.201464 TCACAAACGGATGTATGTAGACATATT 58.799 33.333 5.69 0.00 40.18 1.28
1853 2949 7.722363 TCACAAACGGATGTATGTAGACATAT 58.278 34.615 5.69 0.00 40.18 1.78
1854 2950 7.102847 TCACAAACGGATGTATGTAGACATA 57.897 36.000 0.00 0.00 40.18 2.29
1855 2951 5.972935 TCACAAACGGATGTATGTAGACAT 58.027 37.500 0.08 0.08 42.82 3.06
1856 2952 5.394224 TCACAAACGGATGTATGTAGACA 57.606 39.130 0.00 0.00 30.84 3.41
1857 2953 7.201145 ACTATCACAAACGGATGTATGTAGAC 58.799 38.462 11.58 0.00 30.84 2.59
1858 2954 7.067737 TGACTATCACAAACGGATGTATGTAGA 59.932 37.037 11.58 1.32 30.84 2.59
1859 2955 7.200455 TGACTATCACAAACGGATGTATGTAG 58.800 38.462 0.00 2.34 30.84 2.74
1860 2956 7.102847 TGACTATCACAAACGGATGTATGTA 57.897 36.000 0.00 0.00 30.84 2.29
1861 2957 5.972935 TGACTATCACAAACGGATGTATGT 58.027 37.500 0.00 0.00 30.84 2.29
1862 2958 7.482654 AATGACTATCACAAACGGATGTATG 57.517 36.000 0.00 0.00 30.84 2.39
1863 2959 7.768582 TCAAATGACTATCACAAACGGATGTAT 59.231 33.333 0.00 0.00 30.84 2.29
1864 2960 7.100409 TCAAATGACTATCACAAACGGATGTA 58.900 34.615 0.00 0.00 30.84 2.29
1865 2961 5.937540 TCAAATGACTATCACAAACGGATGT 59.062 36.000 0.00 0.00 0.00 3.06
1866 2962 6.421377 TCAAATGACTATCACAAACGGATG 57.579 37.500 0.00 0.00 0.00 3.51
1867 2963 7.447374 TTTCAAATGACTATCACAAACGGAT 57.553 32.000 0.00 0.00 0.00 4.18
1868 2964 6.869315 TTTCAAATGACTATCACAAACGGA 57.131 33.333 0.00 0.00 0.00 4.69
1869 2965 6.033831 GCATTTCAAATGACTATCACAAACGG 59.966 38.462 14.65 0.00 0.00 4.44
1870 2966 6.033831 GGCATTTCAAATGACTATCACAAACG 59.966 38.462 14.65 0.00 0.00 3.60
1871 2967 7.092716 AGGCATTTCAAATGACTATCACAAAC 58.907 34.615 17.52 0.00 35.20 2.93
1872 2968 7.230849 AGGCATTTCAAATGACTATCACAAA 57.769 32.000 17.52 0.00 35.20 2.83
1873 2969 6.839124 AGGCATTTCAAATGACTATCACAA 57.161 33.333 17.52 0.00 35.20 3.33
1874 2970 7.337938 TCTAGGCATTTCAAATGACTATCACA 58.662 34.615 23.50 5.75 38.80 3.58
1875 2971 7.792374 TCTAGGCATTTCAAATGACTATCAC 57.208 36.000 23.50 0.15 38.80 3.06
1876 2972 8.806429 TTTCTAGGCATTTCAAATGACTATCA 57.194 30.769 23.50 12.23 38.80 2.15
1877 2973 9.113838 TCTTTCTAGGCATTTCAAATGACTATC 57.886 33.333 23.50 1.52 38.80 2.08
1878 2974 8.897752 GTCTTTCTAGGCATTTCAAATGACTAT 58.102 33.333 23.50 4.64 38.80 2.12
1879 2975 7.882791 TGTCTTTCTAGGCATTTCAAATGACTA 59.117 33.333 22.19 22.19 38.54 2.59
1880 2976 6.716628 TGTCTTTCTAGGCATTTCAAATGACT 59.283 34.615 22.35 22.35 41.04 3.41
1881 2977 6.913170 TGTCTTTCTAGGCATTTCAAATGAC 58.087 36.000 14.65 11.48 29.10 3.06
1882 2978 7.231317 ACTTGTCTTTCTAGGCATTTCAAATGA 59.769 33.333 14.65 0.00 35.56 2.57
1883 2979 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
1884 2980 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
1885 2981 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
1886 2982 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
1887 2983 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
1889 2985 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
1890 2986 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
1891 2987 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
1892 2988 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
1893 2989 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
1894 2990 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
1895 2991 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
1896 2992 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
1897 2993 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
1898 2994 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
1899 2995 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
1900 2996 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1901 2997 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
1902 2998 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
1903 2999 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1904 3000 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1905 3001 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1906 3002 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1907 3003 4.261363 CGTACTCCCTCCGTTCCTAAATAC 60.261 50.000 0.00 0.00 0.00 1.89
1908 3004 3.885297 CGTACTCCCTCCGTTCCTAAATA 59.115 47.826 0.00 0.00 0.00 1.40
1909 3005 2.692041 CGTACTCCCTCCGTTCCTAAAT 59.308 50.000 0.00 0.00 0.00 1.40
1910 3006 2.094675 CGTACTCCCTCCGTTCCTAAA 58.905 52.381 0.00 0.00 0.00 1.85
1911 3007 1.004745 ACGTACTCCCTCCGTTCCTAA 59.995 52.381 0.00 0.00 0.00 2.69
1912 3008 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
1913 3009 0.620556 TACGTACTCCCTCCGTTCCT 59.379 55.000 0.00 0.00 36.12 3.36
1914 3010 0.735471 GTACGTACTCCCTCCGTTCC 59.265 60.000 18.47 0.00 36.12 3.62
1915 3011 1.453155 TGTACGTACTCCCTCCGTTC 58.547 55.000 25.12 0.00 36.12 3.95
1916 3012 1.909700 TTGTACGTACTCCCTCCGTT 58.090 50.000 25.12 0.00 36.12 4.44
1917 3013 2.134789 ATTGTACGTACTCCCTCCGT 57.865 50.000 25.12 0.00 38.53 4.69
1918 3014 2.165030 ACAATTGTACGTACTCCCTCCG 59.835 50.000 25.12 10.43 0.00 4.63
1919 3015 3.881937 ACAATTGTACGTACTCCCTCC 57.118 47.619 25.12 0.00 0.00 4.30
1952 3065 6.773638 AGGAAACATCAACACTCTCTTACAT 58.226 36.000 0.00 0.00 0.00 2.29
1953 3066 6.174720 AGGAAACATCAACACTCTCTTACA 57.825 37.500 0.00 0.00 0.00 2.41
1973 3087 5.681639 AGAGTCTCCGAAAAAGAAAAAGGA 58.318 37.500 0.00 0.00 0.00 3.36
2037 3185 4.689345 CGTCCGTTTTTGTTCCTAGAAGAT 59.311 41.667 0.00 0.00 0.00 2.40
2042 3190 3.387397 ACTCGTCCGTTTTTGTTCCTAG 58.613 45.455 0.00 0.00 0.00 3.02
2050 3206 3.264104 TGTGAAGAACTCGTCCGTTTTT 58.736 40.909 0.00 0.00 0.00 1.94
2090 3259 9.919416 TGATCCAATCTCATTTCTACCATTAAA 57.081 29.630 0.00 0.00 0.00 1.52
2091 3260 9.919416 TTGATCCAATCTCATTTCTACCATTAA 57.081 29.630 0.00 0.00 0.00 1.40
2092 3261 9.919416 TTTGATCCAATCTCATTTCTACCATTA 57.081 29.630 0.00 0.00 0.00 1.90
2093 3262 8.827832 TTTGATCCAATCTCATTTCTACCATT 57.172 30.769 0.00 0.00 0.00 3.16
2131 3301 5.560966 ACCGGCTCTTTGTTTATGTATTG 57.439 39.130 0.00 0.00 0.00 1.90
2151 3321 1.239347 GCTTGACCCAGACAAGAACC 58.761 55.000 10.29 0.00 44.92 3.62
2209 3379 9.713713 GTCTCTGTTAAAATTCCTCTCTTAACT 57.286 33.333 8.76 0.00 35.96 2.24
2217 3387 3.374367 GCGGGTCTCTGTTAAAATTCCTC 59.626 47.826 0.00 0.00 0.00 3.71
2218 3388 3.244770 TGCGGGTCTCTGTTAAAATTCCT 60.245 43.478 0.00 0.00 0.00 3.36
2219 3389 3.078837 TGCGGGTCTCTGTTAAAATTCC 58.921 45.455 0.00 0.00 0.00 3.01
2220 3390 4.379499 CCTTGCGGGTCTCTGTTAAAATTC 60.379 45.833 0.00 0.00 0.00 2.17
2221 3391 3.506067 CCTTGCGGGTCTCTGTTAAAATT 59.494 43.478 0.00 0.00 0.00 1.82
2222 3392 3.081804 CCTTGCGGGTCTCTGTTAAAAT 58.918 45.455 0.00 0.00 0.00 1.82
2223 3393 2.500229 CCTTGCGGGTCTCTGTTAAAA 58.500 47.619 0.00 0.00 0.00 1.52
2224 3394 1.880646 GCCTTGCGGGTCTCTGTTAAA 60.881 52.381 0.00 0.00 37.43 1.52
2225 3395 0.321298 GCCTTGCGGGTCTCTGTTAA 60.321 55.000 0.00 0.00 37.43 2.01
2226 3396 1.295423 GCCTTGCGGGTCTCTGTTA 59.705 57.895 0.00 0.00 37.43 2.41
2227 3397 2.032681 GCCTTGCGGGTCTCTGTT 59.967 61.111 0.00 0.00 37.43 3.16
2240 3410 2.043227 CTTATCTCTTCTCCCCGCCTT 58.957 52.381 0.00 0.00 0.00 4.35
2249 3419 6.830838 CCTTTTTATGGGCACTTATCTCTTCT 59.169 38.462 0.00 0.00 0.00 2.85
2250 3420 6.039829 CCCTTTTTATGGGCACTTATCTCTTC 59.960 42.308 0.00 0.00 37.99 2.87
2265 3441 5.982890 TCAAAGAGAAGGCCCTTTTTATG 57.017 39.130 0.00 0.00 30.89 1.90
2266 3442 5.658634 GGATCAAAGAGAAGGCCCTTTTTAT 59.341 40.000 0.00 0.00 30.89 1.40
2267 3443 5.016831 GGATCAAAGAGAAGGCCCTTTTTA 58.983 41.667 0.00 0.00 30.89 1.52
2279 3498 4.021229 TGTTACCGCTAGGATCAAAGAGA 58.979 43.478 0.00 0.00 41.02 3.10
2337 3556 5.163478 GGAGCTTTGAAATGAGCATACCATT 60.163 40.000 0.00 0.00 41.31 3.16
2338 3557 4.340381 GGAGCTTTGAAATGAGCATACCAT 59.660 41.667 0.00 0.00 41.31 3.55
2341 3560 3.696051 TGGGAGCTTTGAAATGAGCATAC 59.304 43.478 0.00 0.00 41.31 2.39
2352 3571 1.774254 TCTGTTTCCTGGGAGCTTTGA 59.226 47.619 0.00 0.00 0.00 2.69
2371 3590 2.744202 CCCTCACTTACTTGTGCATGTC 59.256 50.000 0.00 0.00 37.81 3.06
2372 3591 2.783135 CCCTCACTTACTTGTGCATGT 58.217 47.619 0.00 0.00 37.81 3.21
2466 3685 4.688879 GTCTCAACAATGACATTACCACGA 59.311 41.667 0.00 0.00 33.75 4.35
2535 3754 2.760374 CGCCTCACCTTCTATTCCATC 58.240 52.381 0.00 0.00 0.00 3.51
2569 3788 1.228644 TTGCCCACTCTGCAAGCAT 60.229 52.632 0.00 0.00 43.36 3.79
2640 3859 3.154710 GTCAGGGGGAAGAATCGTTTTT 58.845 45.455 0.00 0.00 0.00 1.94
2641 3860 2.107552 TGTCAGGGGGAAGAATCGTTTT 59.892 45.455 0.00 0.00 0.00 2.43
2642 3861 1.702957 TGTCAGGGGGAAGAATCGTTT 59.297 47.619 0.00 0.00 0.00 3.60
2643 3862 1.279271 CTGTCAGGGGGAAGAATCGTT 59.721 52.381 0.00 0.00 0.00 3.85
2644 3863 0.905357 CTGTCAGGGGGAAGAATCGT 59.095 55.000 0.00 0.00 0.00 3.73
2645 3864 0.462759 GCTGTCAGGGGGAAGAATCG 60.463 60.000 1.14 0.00 0.00 3.34
2646 3865 0.915364 AGCTGTCAGGGGGAAGAATC 59.085 55.000 1.14 0.00 0.00 2.52
2647 3866 0.622665 CAGCTGTCAGGGGGAAGAAT 59.377 55.000 5.25 0.00 0.00 2.40
2648 3867 1.492133 CCAGCTGTCAGGGGGAAGAA 61.492 60.000 13.81 0.00 0.00 2.52
2649 3868 1.920325 CCAGCTGTCAGGGGGAAGA 60.920 63.158 13.81 0.00 0.00 2.87
2650 3869 2.673523 CCAGCTGTCAGGGGGAAG 59.326 66.667 13.81 0.00 0.00 3.46
2651 3870 2.935481 CCCAGCTGTCAGGGGGAA 60.935 66.667 13.81 0.00 43.57 3.97
2653 3872 3.721706 GTCCCAGCTGTCAGGGGG 61.722 72.222 13.81 5.50 45.51 5.40
2654 3873 3.721706 GGTCCCAGCTGTCAGGGG 61.722 72.222 13.81 6.32 45.51 4.79
2655 3874 3.721706 GGGTCCCAGCTGTCAGGG 61.722 72.222 13.81 6.75 46.90 4.45
2656 3875 2.930019 TGGGTCCCAGCTGTCAGG 60.930 66.667 13.81 7.08 0.00 3.86
2657 3876 2.348998 GTGGGTCCCAGCTGTCAG 59.651 66.667 12.21 0.78 32.34 3.51
2665 3884 1.223077 AGATATAGCTGGTGGGTCCCA 59.777 52.381 6.47 6.47 34.77 4.37
2666 3885 2.031495 AGATATAGCTGGTGGGTCCC 57.969 55.000 0.00 0.00 34.77 4.46
2667 3886 2.972713 TGAAGATATAGCTGGTGGGTCC 59.027 50.000 0.00 0.00 0.00 4.46
2668 3887 3.388024 TGTGAAGATATAGCTGGTGGGTC 59.612 47.826 0.00 0.00 0.00 4.46
2669 3888 3.134804 GTGTGAAGATATAGCTGGTGGGT 59.865 47.826 0.00 0.00 0.00 4.51
2670 3889 3.733337 GTGTGAAGATATAGCTGGTGGG 58.267 50.000 0.00 0.00 0.00 4.61
2671 3890 3.384668 CGTGTGAAGATATAGCTGGTGG 58.615 50.000 0.00 0.00 0.00 4.61
2672 3891 3.068165 TCCGTGTGAAGATATAGCTGGTG 59.932 47.826 0.00 0.00 0.00 4.17
2673 3892 3.296854 TCCGTGTGAAGATATAGCTGGT 58.703 45.455 0.00 0.00 0.00 4.00
2674 3893 4.322080 TTCCGTGTGAAGATATAGCTGG 57.678 45.455 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.