Multiple sequence alignment - TraesCS3D01G216800

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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 TraesCS3D01G216800 chr3D 100.000 2290 0 0 1 2290 294145945 294148234 0.000000e+00 4229
1 TraesCS3D01G216800 chr3D 94.395 446 24 1 1846 2290 99135263 99134818 0.000000e+00 684
2 TraesCS3D01G216800 chr3D 82.917 480 63 10 844 1312 177030968 177030497 4.550000e-112 414
3 TraesCS3D01G216800 chr3D 85.559 367 43 9 1480 1839 236657204 236657567 2.150000e-100 375
4 TraesCS3D01G216800 chr3D 81.019 432 77 4 875 1301 497654041 497653610 2.820000e-89 339
5 TraesCS3D01G216800 chr3D 81.436 404 68 5 842 1242 88434097 88433698 7.890000e-85 324
6 TraesCS3D01G216800 chr3D 81.250 336 54 8 1517 1845 140410294 140410627 1.740000e-66 263
7 TraesCS3D01G216800 chr3A 92.411 1186 84 2 842 2022 388952114 388953298 0.000000e+00 1687
8 TraesCS3D01G216800 chr3A 92.747 455 28 4 1839 2290 296134530 296134982 0.000000e+00 652
9 TraesCS3D01G216800 chr3A 83.333 474 63 7 848 1312 217724394 217723928 7.560000e-115 424
10 TraesCS3D01G216800 chr3A 85.792 366 42 8 1480 1838 323404629 323404267 1.660000e-101 379
11 TraesCS3D01G216800 chr3A 82.558 344 50 9 1510 1845 158161775 158162116 6.190000e-76 294
12 TraesCS3D01G216800 chr3A 75.000 416 97 7 885 1297 502175634 502175223 3.880000e-43 185
13 TraesCS3D01G216800 chr6D 93.499 846 50 5 1 842 176366568 176367412 0.000000e+00 1253
14 TraesCS3D01G216800 chr6D 93.274 446 28 2 1846 2290 178018848 178019292 0.000000e+00 656
15 TraesCS3D01G216800 chr1D 92.908 846 53 7 1 841 326992619 326993462 0.000000e+00 1223
16 TraesCS3D01G216800 chr1D 92.899 845 54 6 1 841 492878580 492877738 0.000000e+00 1223
17 TraesCS3D01G216800 chr1D 92.580 849 58 5 1 845 431343118 431342271 0.000000e+00 1214
18 TraesCS3D01G216800 chr1D 92.571 848 53 6 1 841 181565648 181566492 0.000000e+00 1208
19 TraesCS3D01G216800 chr1D 92.544 845 56 7 2 841 134493187 134492345 0.000000e+00 1205
20 TraesCS3D01G216800 chr1D 92.408 461 33 2 1832 2290 164786032 164786492 0.000000e+00 656
21 TraesCS3D01G216800 chr1D 82.203 354 55 6 842 1192 182636851 182637199 4.780000e-77 298
22 TraesCS3D01G216800 chr2D 92.680 847 57 5 1 845 386242475 386243318 0.000000e+00 1216
23 TraesCS3D01G216800 chr4D 92.764 843 54 6 1 840 27686243 27687081 0.000000e+00 1212
24 TraesCS3D01G216800 chr4D 93.274 446 29 1 1846 2290 21984787 21985232 0.000000e+00 656
25 TraesCS3D01G216800 chr5D 92.371 852 54 8 1 843 114629080 114628231 0.000000e+00 1203
26 TraesCS3D01G216800 chr5D 93.933 445 27 0 1846 2290 459058967 459058523 0.000000e+00 673
27 TraesCS3D01G216800 chr5D 93.258 445 29 1 1846 2290 93787954 93787511 0.000000e+00 654
28 TraesCS3D01G216800 chr5D 93.080 448 27 4 1845 2290 101949770 101949325 0.000000e+00 652
29 TraesCS3D01G216800 chr3B 89.779 949 83 4 842 1778 387913976 387914922 0.000000e+00 1203
30 TraesCS3D01G216800 chr7D 93.049 446 30 1 1846 2290 411880488 411880043 0.000000e+00 651
31 TraesCS3D01G216800 chr7D 80.789 380 58 8 1475 1845 432431808 432431435 1.340000e-72 283
32 TraesCS3D01G216800 chr7A 82.561 367 56 8 1480 1839 272239195 272238830 1.320000e-82 316
33 TraesCS3D01G216800 chr4A 79.859 427 81 5 878 1301 553467641 553467217 7.950000e-80 307
34 TraesCS3D01G216800 chr4A 81.351 370 56 12 1478 1839 92746616 92746980 2.880000e-74 289
35 TraesCS3D01G216800 chr4A 78.972 428 83 7 878 1301 4144951 4144527 3.720000e-73 285
36 TraesCS3D01G216800 chr2B 79.070 430 80 9 874 1296 625420459 625420033 1.040000e-73 287
37 TraesCS3D01G216800 chr7B 79.063 363 63 8 1485 1838 172623751 172624109 1.060000e-58 237


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 TraesCS3D01G216800 chr3D 294145945 294148234 2289 False 4229 4229 100.000 1 2290 1 chr3D.!!$F3 2289
1 TraesCS3D01G216800 chr3A 388952114 388953298 1184 False 1687 1687 92.411 842 2022 1 chr3A.!!$F3 1180
2 TraesCS3D01G216800 chr6D 176366568 176367412 844 False 1253 1253 93.499 1 842 1 chr6D.!!$F1 841
3 TraesCS3D01G216800 chr1D 326992619 326993462 843 False 1223 1223 92.908 1 841 1 chr1D.!!$F4 840
4 TraesCS3D01G216800 chr1D 492877738 492878580 842 True 1223 1223 92.899 1 841 1 chr1D.!!$R3 840
5 TraesCS3D01G216800 chr1D 431342271 431343118 847 True 1214 1214 92.580 1 845 1 chr1D.!!$R2 844
6 TraesCS3D01G216800 chr1D 181565648 181566492 844 False 1208 1208 92.571 1 841 1 chr1D.!!$F2 840
7 TraesCS3D01G216800 chr1D 134492345 134493187 842 True 1205 1205 92.544 2 841 1 chr1D.!!$R1 839
8 TraesCS3D01G216800 chr2D 386242475 386243318 843 False 1216 1216 92.680 1 845 1 chr2D.!!$F1 844
9 TraesCS3D01G216800 chr4D 27686243 27687081 838 False 1212 1212 92.764 1 840 1 chr4D.!!$F2 839
10 TraesCS3D01G216800 chr5D 114628231 114629080 849 True 1203 1203 92.371 1 843 1 chr5D.!!$R3 842
11 TraesCS3D01G216800 chr3B 387913976 387914922 946 False 1203 1203 89.779 842 1778 1 chr3B.!!$F1 936

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
21 23 0.326048 ATGTCAGGCTGCTCCTAGGT 60.326 55.0 10.34 0.0 45.52 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1815 0.041312 ACACGCTTCAACGCATGTTC 60.041 50.0 0.0 0.0 35.72 3.18 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
21 23 0.326048 ATGTCAGGCTGCTCCTAGGT 60.326 55.000 10.34 0.00 45.52 3.08
43 47 0.760572 TAAATAGCCGCCCCCTACAC 59.239 55.000 0.00 0.00 0.00 2.90
119 124 3.768008 TCCTCCGAGGACTTTGAGT 57.232 52.632 13.54 0.00 40.06 3.41
138 144 5.485620 TGAGTGAAAATCATCAGTGAGGAG 58.514 41.667 13.58 0.00 35.16 3.69
166 174 2.830651 ACCCAAACACCTACAAACCA 57.169 45.000 0.00 0.00 0.00 3.67
178 187 5.530915 CACCTACAAACCAAAGTGATTGAGA 59.469 40.000 0.00 0.00 41.85 3.27
304 313 2.678580 TGGATCGCCGAGTGACCA 60.679 61.111 0.00 0.00 36.79 4.02
347 356 1.272769 ACCTGAAGACTTACCACGAGC 59.727 52.381 0.00 0.00 0.00 5.03
417 427 3.805207 ACTGTGTGTCCTCAGGTTAAAC 58.195 45.455 0.00 0.00 36.68 2.01
439 449 1.690219 CCTAGCCGCTCCAACCAGAT 61.690 60.000 0.00 0.00 0.00 2.90
448 458 2.426024 GCTCCAACCAGATGTACGACTA 59.574 50.000 0.00 0.00 0.00 2.59
553 563 8.564509 TCATTCATGTGTTGATGAACTTGATA 57.435 30.769 0.00 0.00 43.45 2.15
557 567 7.809665 TCATGTGTTGATGAACTTGATAGTTG 58.190 34.615 0.00 0.00 44.51 3.16
630 640 4.584743 TCTTCAGTCACTTAGTCTTCAGCA 59.415 41.667 0.00 0.00 0.00 4.41
718 729 3.379372 ACTGTTCTGTTATGCATGCATCC 59.621 43.478 35.35 25.77 37.82 3.51
752 763 2.066262 GCTGCTAAGTAGTTCGTTGCA 58.934 47.619 0.00 0.00 35.60 4.08
795 806 5.613358 AATTCCTCAGTGACGAATTTGTC 57.387 39.130 18.73 17.60 33.50 3.18
973 990 2.079158 TGACAGCTGAAGCATTAGCAC 58.921 47.619 23.35 0.43 45.49 4.40
1001 1018 1.901159 TGGCTTATTGCTGGCACAAAT 59.099 42.857 6.60 1.77 38.70 2.32
1010 1027 2.753849 GGCACAAATGGCGGGCTA 60.754 61.111 2.38 0.00 42.22 3.93
1192 1209 2.053244 AGTAGCCCATGAGCTTGCTAT 58.947 47.619 7.16 0.00 41.41 2.97
1224 1241 2.890311 TGTTCCATGAAAAGCGATTGGT 59.110 40.909 0.00 0.00 0.00 3.67
1368 1386 0.673644 CCGCTTTCGAACCATCCACT 60.674 55.000 0.00 0.00 38.10 4.00
1396 1414 0.107752 TGCCATTCAGAGCATACGCA 60.108 50.000 0.00 0.00 42.27 5.24
1400 1418 1.004610 CATTCAGAGCATACGCAACCG 60.005 52.381 0.00 0.00 42.27 4.44
1426 1444 2.954318 GCCTCCTACATGCATTGATGTT 59.046 45.455 0.00 0.00 37.70 2.71
1512 1530 1.048724 CCGGCAGATCTTGGGTAGGA 61.049 60.000 0.00 0.00 0.00 2.94
1517 1535 2.043227 CAGATCTTGGGTAGGAGGTCC 58.957 57.143 0.00 0.00 0.00 4.46
1518 1536 1.062044 AGATCTTGGGTAGGAGGTCCC 60.062 57.143 0.00 0.00 43.67 4.46
1552 1570 7.093068 TGGTCTTGGCTAGATAGTAACATGAAA 60.093 37.037 0.00 0.00 34.79 2.69
1669 1697 3.304123 GGTTCATCTACCTCGAGATCGTG 60.304 52.174 15.71 6.25 40.80 4.35
1695 1723 7.394872 CGAATGAGTCTAAAAGATTTTCCTCG 58.605 38.462 0.00 0.00 0.00 4.63
1704 1732 8.198109 TCTAAAAGATTTTCCTCGATGGACTAG 58.802 37.037 3.44 0.00 46.14 2.57
1762 1790 4.890581 GGGTTATACATGGTTGGTTGCATA 59.109 41.667 0.00 0.00 0.00 3.14
1792 1820 9.985730 AGACAAACATGTTGAATATTTGAACAT 57.014 25.926 12.82 15.83 40.20 2.71
1798 1826 6.687653 TGTTGAATATTTGAACATGCGTTG 57.312 33.333 8.99 0.00 34.75 4.10
1799 1827 6.442112 TGTTGAATATTTGAACATGCGTTGA 58.558 32.000 8.99 0.00 34.75 3.18
1802 1830 5.572511 TGAATATTTGAACATGCGTTGAAGC 59.427 36.000 0.00 0.00 34.75 3.86
1819 1847 2.070861 GCGTGTGCTAAGTCTTCGG 58.929 57.895 0.00 0.00 38.39 4.30
1822 1850 1.711206 GTGTGCTAAGTCTTCGGGAC 58.289 55.000 0.00 0.00 44.80 4.46
1886 1914 4.629634 TCCATGATGATACGTGTTTGTCAC 59.370 41.667 0.00 0.00 43.03 3.67
1924 1952 3.215975 TGTCATGCATGTACATCCATGG 58.784 45.455 30.48 17.15 42.01 3.66
1950 1978 8.768955 GCGATTTTATGACAGAATCAAGATAGT 58.231 33.333 0.00 0.00 41.93 2.12
1972 2000 5.046529 GTCATACCTGTGCTGTCATAGAAG 58.953 45.833 0.00 0.00 33.81 2.85
2025 2053 1.003355 AGTGTCCACTTCCATGCCG 60.003 57.895 0.00 0.00 38.83 5.69
2026 2054 1.003839 GTGTCCACTTCCATGCCGA 60.004 57.895 0.00 0.00 0.00 5.54
2027 2055 0.392998 GTGTCCACTTCCATGCCGAT 60.393 55.000 0.00 0.00 0.00 4.18
2028 2056 1.134521 GTGTCCACTTCCATGCCGATA 60.135 52.381 0.00 0.00 0.00 2.92
2029 2057 1.557371 TGTCCACTTCCATGCCGATAA 59.443 47.619 0.00 0.00 0.00 1.75
2030 2058 2.026729 TGTCCACTTCCATGCCGATAAA 60.027 45.455 0.00 0.00 0.00 1.40
2031 2059 3.214328 GTCCACTTCCATGCCGATAAAT 58.786 45.455 0.00 0.00 0.00 1.40
2032 2060 3.003689 GTCCACTTCCATGCCGATAAATG 59.996 47.826 0.00 0.00 0.00 2.32
2033 2061 2.294233 CCACTTCCATGCCGATAAATGG 59.706 50.000 0.00 0.00 44.06 3.16
2039 2067 2.248431 GCCGATAAATGGCGCGTC 59.752 61.111 2.29 2.29 43.70 5.19
2040 2068 2.544359 CCGATAAATGGCGCGTCG 59.456 61.111 6.09 6.10 0.00 5.12
2041 2069 2.235016 CCGATAAATGGCGCGTCGT 61.235 57.895 6.09 1.35 0.00 4.34
2042 2070 1.084290 CGATAAATGGCGCGTCGTG 60.084 57.895 6.02 0.25 0.00 4.35
2043 2071 1.275657 GATAAATGGCGCGTCGTGG 59.724 57.895 6.02 0.00 0.00 4.94
2044 2072 1.149361 GATAAATGGCGCGTCGTGGA 61.149 55.000 6.02 0.00 0.00 4.02
2045 2073 0.741574 ATAAATGGCGCGTCGTGGAA 60.742 50.000 6.02 0.00 0.00 3.53
2046 2074 1.355796 TAAATGGCGCGTCGTGGAAG 61.356 55.000 6.02 0.00 0.00 3.46
2047 2075 3.876589 AATGGCGCGTCGTGGAAGT 62.877 57.895 6.02 0.00 0.00 3.01
2051 2079 3.036084 CGCGTCGTGGAAGTGCTT 61.036 61.111 0.00 0.00 0.00 3.91
2052 2080 2.594962 CGCGTCGTGGAAGTGCTTT 61.595 57.895 0.00 0.00 0.00 3.51
2053 2081 1.204312 GCGTCGTGGAAGTGCTTTC 59.796 57.895 0.00 0.00 34.93 2.62
2054 2082 1.487231 CGTCGTGGAAGTGCTTTCG 59.513 57.895 0.00 0.00 36.62 3.46
2055 2083 1.213094 CGTCGTGGAAGTGCTTTCGT 61.213 55.000 0.00 0.00 36.62 3.85
2056 2084 0.507358 GTCGTGGAAGTGCTTTCGTC 59.493 55.000 0.00 0.00 36.62 4.20
2057 2085 0.103390 TCGTGGAAGTGCTTTCGTCA 59.897 50.000 0.00 0.00 36.62 4.35
2058 2086 0.934496 CGTGGAAGTGCTTTCGTCAA 59.066 50.000 0.00 0.00 36.62 3.18
2059 2087 1.070577 CGTGGAAGTGCTTTCGTCAAG 60.071 52.381 0.00 0.00 36.62 3.02
2060 2088 1.264288 GTGGAAGTGCTTTCGTCAAGG 59.736 52.381 0.00 0.00 36.62 3.61
2061 2089 0.875059 GGAAGTGCTTTCGTCAAGGG 59.125 55.000 0.00 0.00 36.62 3.95
2062 2090 1.594331 GAAGTGCTTTCGTCAAGGGT 58.406 50.000 0.00 0.00 32.37 4.34
2063 2091 2.549349 GGAAGTGCTTTCGTCAAGGGTA 60.549 50.000 0.00 0.00 36.62 3.69
2064 2092 2.922740 AGTGCTTTCGTCAAGGGTAA 57.077 45.000 0.00 0.00 32.37 2.85
2065 2093 2.490991 AGTGCTTTCGTCAAGGGTAAC 58.509 47.619 0.00 0.00 32.37 2.50
2077 2105 4.705746 GGTAACCGACACATGGCA 57.294 55.556 0.00 0.00 0.00 4.92
2078 2106 3.168773 GGTAACCGACACATGGCAT 57.831 52.632 0.00 0.00 0.00 4.40
2079 2107 1.014352 GGTAACCGACACATGGCATC 58.986 55.000 0.00 0.00 0.00 3.91
2080 2108 1.014352 GTAACCGACACATGGCATCC 58.986 55.000 0.00 0.00 0.00 3.51
2081 2109 0.615850 TAACCGACACATGGCATCCA 59.384 50.000 0.00 0.00 38.19 3.41
2082 2110 0.034186 AACCGACACATGGCATCCAT 60.034 50.000 0.00 0.00 46.37 3.41
2083 2111 0.464373 ACCGACACATGGCATCCATC 60.464 55.000 0.00 0.00 43.15 3.51
2084 2112 1.501337 CCGACACATGGCATCCATCG 61.501 60.000 13.91 13.91 43.15 3.84
2085 2113 0.811219 CGACACATGGCATCCATCGT 60.811 55.000 13.04 0.00 43.15 3.73
2086 2114 1.537990 CGACACATGGCATCCATCGTA 60.538 52.381 13.04 0.00 43.15 3.43
2087 2115 2.560504 GACACATGGCATCCATCGTAA 58.439 47.619 0.00 0.00 43.15 3.18
2088 2116 2.287915 GACACATGGCATCCATCGTAAC 59.712 50.000 0.00 0.00 43.15 2.50
2089 2117 1.261354 CACATGGCATCCATCGTAACG 59.739 52.381 0.00 0.00 43.15 3.18
2090 2118 0.867746 CATGGCATCCATCGTAACGG 59.132 55.000 0.00 0.00 43.15 4.44
2091 2119 0.250295 ATGGCATCCATCGTAACGGG 60.250 55.000 0.00 0.00 40.74 5.28
2092 2120 1.145377 GGCATCCATCGTAACGGGT 59.855 57.895 0.00 0.00 0.00 5.28
2093 2121 0.878961 GGCATCCATCGTAACGGGTC 60.879 60.000 0.00 0.00 0.00 4.46
2094 2122 0.179094 GCATCCATCGTAACGGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
2095 2123 1.567504 CATCCATCGTAACGGGTCAC 58.432 55.000 0.00 0.00 0.00 3.67
2096 2124 0.462789 ATCCATCGTAACGGGTCACC 59.537 55.000 0.00 0.00 0.00 4.02
2109 2137 2.285977 GGGTCACCGTTAAGCTATTGG 58.714 52.381 0.00 0.00 0.00 3.16
2110 2138 2.285977 GGTCACCGTTAAGCTATTGGG 58.714 52.381 0.00 0.00 0.00 4.12
2111 2139 2.355412 GGTCACCGTTAAGCTATTGGGT 60.355 50.000 0.00 0.00 0.00 4.51
2112 2140 3.340928 GTCACCGTTAAGCTATTGGGTT 58.659 45.455 0.00 0.00 39.19 4.11
2113 2141 3.373130 GTCACCGTTAAGCTATTGGGTTC 59.627 47.826 0.00 0.00 36.91 3.62
2114 2142 2.681344 CACCGTTAAGCTATTGGGTTCC 59.319 50.000 0.00 0.00 36.91 3.62
2115 2143 1.937899 CCGTTAAGCTATTGGGTTCCG 59.062 52.381 0.00 0.00 36.91 4.30
2116 2144 1.937899 CGTTAAGCTATTGGGTTCCGG 59.062 52.381 0.00 0.00 36.91 5.14
2117 2145 2.678769 CGTTAAGCTATTGGGTTCCGGT 60.679 50.000 0.00 0.00 36.91 5.28
2118 2146 3.349927 GTTAAGCTATTGGGTTCCGGTT 58.650 45.455 0.00 0.00 36.91 4.44
2119 2147 2.597578 AAGCTATTGGGTTCCGGTTT 57.402 45.000 0.00 0.00 0.00 3.27
2120 2148 1.834188 AGCTATTGGGTTCCGGTTTG 58.166 50.000 0.00 0.00 0.00 2.93
2121 2149 0.815095 GCTATTGGGTTCCGGTTTGG 59.185 55.000 0.00 0.00 40.09 3.28
2132 2160 3.553828 TCCGGTTTGGATCTGATAACC 57.446 47.619 0.00 9.73 43.74 2.85
2133 2161 2.171870 TCCGGTTTGGATCTGATAACCC 59.828 50.000 12.83 1.99 43.74 4.11
2134 2162 2.210116 CGGTTTGGATCTGATAACCCG 58.790 52.381 12.83 5.33 37.36 5.28
2135 2163 2.419574 CGGTTTGGATCTGATAACCCGT 60.420 50.000 12.83 0.00 37.36 5.28
2136 2164 3.617284 GGTTTGGATCTGATAACCCGTT 58.383 45.455 8.90 0.00 35.17 4.44
2137 2165 4.681244 CGGTTTGGATCTGATAACCCGTTA 60.681 45.833 12.83 0.00 37.36 3.18
2138 2166 5.187687 GGTTTGGATCTGATAACCCGTTAA 58.812 41.667 8.90 0.00 35.17 2.01
2139 2167 5.065602 GGTTTGGATCTGATAACCCGTTAAC 59.934 44.000 8.90 0.00 35.17 2.01
2140 2168 5.423704 TTGGATCTGATAACCCGTTAACA 57.576 39.130 6.39 0.00 0.00 2.41
2141 2169 5.018539 TGGATCTGATAACCCGTTAACAG 57.981 43.478 15.15 15.15 43.20 3.16
2142 2170 3.808174 GGATCTGATAACCCGTTAACAGC 59.192 47.826 16.05 6.86 42.24 4.40
2143 2171 3.255969 TCTGATAACCCGTTAACAGCC 57.744 47.619 16.05 0.00 42.24 4.85
2144 2172 2.093341 TCTGATAACCCGTTAACAGCCC 60.093 50.000 16.05 0.00 42.24 5.19
2145 2173 1.292992 GATAACCCGTTAACAGCCCG 58.707 55.000 6.39 0.00 0.00 6.13
2146 2174 0.107557 ATAACCCGTTAACAGCCCGG 60.108 55.000 6.39 0.00 41.37 5.73
2147 2175 1.190833 TAACCCGTTAACAGCCCGGA 61.191 55.000 0.73 0.00 44.41 5.14
2148 2176 2.435410 CCCGTTAACAGCCCGGAC 60.435 66.667 0.73 0.00 44.41 4.79
2149 2177 2.435410 CCGTTAACAGCCCGGACC 60.435 66.667 0.73 0.00 44.41 4.46
2150 2178 2.344500 CGTTAACAGCCCGGACCA 59.656 61.111 0.73 0.00 0.00 4.02
2151 2179 1.301874 CGTTAACAGCCCGGACCAA 60.302 57.895 0.73 0.00 0.00 3.67
2152 2180 0.675522 CGTTAACAGCCCGGACCAAT 60.676 55.000 0.73 0.00 0.00 3.16
2153 2181 0.808755 GTTAACAGCCCGGACCAATG 59.191 55.000 0.73 0.00 0.00 2.82
2154 2182 0.322997 TTAACAGCCCGGACCAATGG 60.323 55.000 0.73 0.00 0.00 3.16
2156 2184 4.820744 CAGCCCGGACCAATGGGG 62.821 72.222 0.73 1.66 46.12 4.96
2158 2186 3.820843 GCCCGGACCAATGGGGAT 61.821 66.667 0.73 0.00 46.12 3.85
2159 2187 3.015383 CCCGGACCAATGGGGATT 58.985 61.111 0.73 0.00 44.10 3.01
2160 2188 1.309688 CCCGGACCAATGGGGATTT 59.690 57.895 0.73 0.00 44.10 2.17
2161 2189 0.325203 CCCGGACCAATGGGGATTTT 60.325 55.000 0.73 0.00 44.10 1.82
2162 2190 1.111277 CCGGACCAATGGGGATTTTC 58.889 55.000 3.55 0.00 41.15 2.29
2163 2191 1.111277 CGGACCAATGGGGATTTTCC 58.889 55.000 3.55 0.00 41.15 3.13
2164 2192 1.618345 CGGACCAATGGGGATTTTCCA 60.618 52.381 3.55 0.00 38.64 3.53
2165 2193 1.831106 GGACCAATGGGGATTTTCCAC 59.169 52.381 3.55 0.00 41.45 4.02
2166 2194 1.476488 GACCAATGGGGATTTTCCACG 59.524 52.381 3.55 0.00 45.00 4.94
2167 2195 1.203125 ACCAATGGGGATTTTCCACGT 60.203 47.619 3.55 0.00 45.00 4.49
2168 2196 1.204467 CCAATGGGGATTTTCCACGTG 59.796 52.381 9.08 9.08 45.00 4.49
2169 2197 1.892474 CAATGGGGATTTTCCACGTGT 59.108 47.619 15.65 0.00 45.00 4.49
2170 2198 3.085533 CAATGGGGATTTTCCACGTGTA 58.914 45.455 15.65 0.00 45.00 2.90
2171 2199 2.953284 TGGGGATTTTCCACGTGTAA 57.047 45.000 15.65 1.07 45.00 2.41
2172 2200 3.225177 TGGGGATTTTCCACGTGTAAA 57.775 42.857 15.65 14.28 45.00 2.01
2173 2201 3.563223 TGGGGATTTTCCACGTGTAAAA 58.437 40.909 19.43 19.43 45.00 1.52
2174 2202 4.153411 TGGGGATTTTCCACGTGTAAAAT 58.847 39.130 25.95 25.95 45.00 1.82
2175 2203 4.589374 TGGGGATTTTCCACGTGTAAAATT 59.411 37.500 26.24 16.53 45.00 1.82
2176 2204 5.773680 TGGGGATTTTCCACGTGTAAAATTA 59.226 36.000 26.24 14.25 45.00 1.40
2177 2205 6.437793 TGGGGATTTTCCACGTGTAAAATTAT 59.562 34.615 26.24 10.99 45.00 1.28
2178 2206 6.976349 GGGGATTTTCCACGTGTAAAATTATC 59.024 38.462 26.24 17.41 38.64 1.75
2179 2207 7.363094 GGGGATTTTCCACGTGTAAAATTATCA 60.363 37.037 26.24 4.85 38.64 2.15
2180 2208 8.030106 GGGATTTTCCACGTGTAAAATTATCAA 58.970 33.333 26.24 4.20 38.64 2.57
2181 2209 9.581099 GGATTTTCCACGTGTAAAATTATCAAT 57.419 29.630 26.24 9.10 35.87 2.57
2183 2211 8.749841 TTTTCCACGTGTAAAATTATCAATGG 57.250 30.769 14.20 0.00 0.00 3.16
2184 2212 5.885881 TCCACGTGTAAAATTATCAATGGC 58.114 37.500 15.65 0.00 0.00 4.40
2185 2213 5.650266 TCCACGTGTAAAATTATCAATGGCT 59.350 36.000 15.65 0.00 0.00 4.75
2186 2214 6.824196 TCCACGTGTAAAATTATCAATGGCTA 59.176 34.615 15.65 0.00 0.00 3.93
2187 2215 7.011950 TCCACGTGTAAAATTATCAATGGCTAG 59.988 37.037 15.65 0.00 0.00 3.42
2188 2216 7.011950 CCACGTGTAAAATTATCAATGGCTAGA 59.988 37.037 15.65 0.00 0.00 2.43
2189 2217 8.064222 CACGTGTAAAATTATCAATGGCTAGAG 58.936 37.037 7.58 0.00 0.00 2.43
2190 2218 7.226720 ACGTGTAAAATTATCAATGGCTAGAGG 59.773 37.037 0.00 0.00 0.00 3.69
2191 2219 7.441157 CGTGTAAAATTATCAATGGCTAGAGGA 59.559 37.037 0.00 0.00 0.00 3.71
2192 2220 9.120538 GTGTAAAATTATCAATGGCTAGAGGAA 57.879 33.333 0.00 0.00 0.00 3.36
2193 2221 9.120538 TGTAAAATTATCAATGGCTAGAGGAAC 57.879 33.333 0.00 0.00 0.00 3.62
2194 2222 7.588497 AAAATTATCAATGGCTAGAGGAACC 57.412 36.000 0.00 0.00 0.00 3.62
2195 2223 5.912149 ATTATCAATGGCTAGAGGAACCA 57.088 39.130 0.00 0.00 37.99 3.67
2196 2224 3.567478 ATCAATGGCTAGAGGAACCAC 57.433 47.619 0.00 0.00 35.99 4.16
2197 2225 1.207089 TCAATGGCTAGAGGAACCACG 59.793 52.381 0.00 0.00 35.99 4.94
2198 2226 1.066143 CAATGGCTAGAGGAACCACGT 60.066 52.381 0.00 0.00 35.99 4.49
2199 2227 0.537188 ATGGCTAGAGGAACCACGTG 59.463 55.000 9.08 9.08 35.99 4.49
2200 2228 0.830444 TGGCTAGAGGAACCACGTGT 60.830 55.000 15.65 0.00 0.00 4.49
2201 2229 0.108756 GGCTAGAGGAACCACGTGTC 60.109 60.000 15.65 6.19 0.00 3.67
2202 2230 0.456312 GCTAGAGGAACCACGTGTCG 60.456 60.000 15.65 2.14 0.00 4.35
2203 2231 0.170561 CTAGAGGAACCACGTGTCGG 59.829 60.000 15.65 1.15 0.00 4.79
2204 2232 1.870055 TAGAGGAACCACGTGTCGGC 61.870 60.000 15.65 2.19 0.00 5.54
2205 2233 3.222354 GAGGAACCACGTGTCGGCT 62.222 63.158 15.65 0.00 0.00 5.52
2206 2234 2.737376 GGAACCACGTGTCGGCTC 60.737 66.667 15.65 0.00 0.00 4.70
2207 2235 2.028484 GAACCACGTGTCGGCTCA 59.972 61.111 15.65 0.00 0.00 4.26
2208 2236 2.022129 GAACCACGTGTCGGCTCAG 61.022 63.158 15.65 0.00 0.00 3.35
2209 2237 4.664677 ACCACGTGTCGGCTCAGC 62.665 66.667 15.65 0.00 0.00 4.26
2212 2240 4.280494 ACGTGTCGGCTCAGCGTT 62.280 61.111 0.00 0.00 31.37 4.84
2213 2241 3.767230 CGTGTCGGCTCAGCGTTG 61.767 66.667 0.00 0.00 0.00 4.10
2214 2242 3.414700 GTGTCGGCTCAGCGTTGG 61.415 66.667 0.00 0.00 0.00 3.77
2215 2243 4.680237 TGTCGGCTCAGCGTTGGG 62.680 66.667 0.00 0.00 0.00 4.12
2216 2244 4.373116 GTCGGCTCAGCGTTGGGA 62.373 66.667 2.12 0.00 0.00 4.37
2217 2245 4.373116 TCGGCTCAGCGTTGGGAC 62.373 66.667 2.12 0.00 0.00 4.46
2218 2246 4.680237 CGGCTCAGCGTTGGGACA 62.680 66.667 5.60 0.00 29.18 4.02
2219 2247 2.743928 GGCTCAGCGTTGGGACAG 60.744 66.667 2.12 0.00 42.39 3.51
2220 2248 2.343758 GCTCAGCGTTGGGACAGA 59.656 61.111 2.12 0.00 42.39 3.41
2221 2249 1.078848 GCTCAGCGTTGGGACAGAT 60.079 57.895 2.12 0.00 42.39 2.90
2222 2250 0.175760 GCTCAGCGTTGGGACAGATA 59.824 55.000 2.12 0.00 42.39 1.98
2223 2251 1.202580 GCTCAGCGTTGGGACAGATAT 60.203 52.381 2.12 0.00 42.39 1.63
2224 2252 2.748605 CTCAGCGTTGGGACAGATATC 58.251 52.381 0.00 0.00 42.39 1.63
2225 2253 2.101415 CTCAGCGTTGGGACAGATATCA 59.899 50.000 5.32 0.00 42.39 2.15
2226 2254 2.700371 TCAGCGTTGGGACAGATATCAT 59.300 45.455 5.32 0.00 42.39 2.45
2227 2255 3.062763 CAGCGTTGGGACAGATATCATC 58.937 50.000 5.32 2.02 42.39 2.92
2228 2256 2.037772 AGCGTTGGGACAGATATCATCC 59.962 50.000 14.81 14.81 42.39 3.51
2229 2257 2.224281 GCGTTGGGACAGATATCATCCA 60.224 50.000 21.44 12.85 42.39 3.41
2230 2258 3.393800 CGTTGGGACAGATATCATCCAC 58.606 50.000 21.44 13.75 42.39 4.02
2231 2259 3.070159 CGTTGGGACAGATATCATCCACT 59.930 47.826 21.44 0.00 42.39 4.00
2232 2260 4.636249 GTTGGGACAGATATCATCCACTC 58.364 47.826 21.44 9.70 42.39 3.51
2233 2261 3.927476 TGGGACAGATATCATCCACTCA 58.073 45.455 21.44 11.56 33.87 3.41
2234 2262 4.496540 TGGGACAGATATCATCCACTCAT 58.503 43.478 21.44 0.00 33.87 2.90
2235 2263 4.909695 TGGGACAGATATCATCCACTCATT 59.090 41.667 21.44 0.00 33.87 2.57
2236 2264 5.221783 TGGGACAGATATCATCCACTCATTG 60.222 44.000 21.44 4.58 33.87 2.82
2237 2265 9.540009 TTGGGACAGATATCATCCACTCATTGG 62.540 44.444 21.44 0.00 44.37 3.16
2245 2273 4.941609 CACTCATTGGACGGGAGG 57.058 61.111 0.00 0.00 32.98 4.30
2246 2274 1.450312 CACTCATTGGACGGGAGGC 60.450 63.158 0.00 0.00 32.98 4.70
2247 2275 2.202932 CTCATTGGACGGGAGGCG 60.203 66.667 0.00 0.00 40.56 5.52
2248 2276 4.467084 TCATTGGACGGGAGGCGC 62.467 66.667 0.00 0.00 40.56 6.53
2252 2280 4.853142 TGGACGGGAGGCGCCTAT 62.853 66.667 32.97 15.88 40.56 2.57
2253 2281 4.301027 GGACGGGAGGCGCCTATG 62.301 72.222 32.97 23.89 40.56 2.23
2254 2282 3.224324 GACGGGAGGCGCCTATGA 61.224 66.667 32.97 0.00 36.66 2.15
2255 2283 2.524394 ACGGGAGGCGCCTATGAT 60.524 61.111 32.97 13.40 36.66 2.45
2256 2284 1.228769 ACGGGAGGCGCCTATGATA 60.229 57.895 32.97 0.00 36.66 2.15
2257 2285 1.215647 CGGGAGGCGCCTATGATAC 59.784 63.158 32.97 16.21 36.66 2.24
2258 2286 1.215647 GGGAGGCGCCTATGATACG 59.784 63.158 32.97 0.00 36.66 3.06
2259 2287 1.533469 GGGAGGCGCCTATGATACGT 61.533 60.000 32.97 3.02 36.66 3.57
2260 2288 0.109226 GGAGGCGCCTATGATACGTC 60.109 60.000 32.97 13.92 0.00 4.34
2261 2289 0.454620 GAGGCGCCTATGATACGTCG 60.455 60.000 32.97 0.00 36.34 5.12
2262 2290 0.887836 AGGCGCCTATGATACGTCGA 60.888 55.000 31.86 0.00 36.34 4.20
2263 2291 0.728466 GGCGCCTATGATACGTCGAC 60.728 60.000 22.15 5.18 0.00 4.20
2264 2292 0.040692 GCGCCTATGATACGTCGACA 60.041 55.000 17.16 0.00 0.00 4.35
2265 2293 1.671469 CGCCTATGATACGTCGACAC 58.329 55.000 17.16 4.35 0.00 3.67
2266 2294 1.003223 CGCCTATGATACGTCGACACA 60.003 52.381 17.16 9.96 0.00 3.72
2267 2295 2.350484 CGCCTATGATACGTCGACACAT 60.350 50.000 17.16 15.86 0.00 3.21
2268 2296 2.980476 GCCTATGATACGTCGACACATG 59.020 50.000 17.16 1.08 0.00 3.21
2269 2297 3.565516 CCTATGATACGTCGACACATGG 58.434 50.000 17.16 15.03 0.00 3.66
2270 2298 1.852942 ATGATACGTCGACACATGGC 58.147 50.000 17.16 0.00 0.00 4.40
2271 2299 0.528470 TGATACGTCGACACATGGCA 59.472 50.000 17.16 2.65 0.00 4.92
2272 2300 0.921347 GATACGTCGACACATGGCAC 59.079 55.000 17.16 0.00 0.00 5.01
2273 2301 0.800683 ATACGTCGACACATGGCACG 60.801 55.000 17.16 0.74 35.04 5.34
2274 2302 2.805999 TACGTCGACACATGGCACGG 62.806 60.000 17.16 0.00 33.84 4.94
2275 2303 3.788766 GTCGACACATGGCACGGC 61.789 66.667 11.55 0.00 0.00 5.68
2285 2313 4.864334 GGCACGGCCCATCAGAGG 62.864 72.222 0.00 0.00 44.06 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 23 3.008266 GTGTAGGGGGCGGCTATTTATAA 59.992 47.826 9.56 0.00 0.00 0.98
119 124 5.707298 GGTTTCTCCTCACTGATGATTTTCA 59.293 40.000 0.00 0.00 33.22 2.69
138 144 1.834896 AGGTGTTTGGGTTTGGGTTTC 59.165 47.619 0.00 0.00 0.00 2.78
178 187 5.704515 CACAGGAACAATCTCTTCAGTGATT 59.295 40.000 0.00 0.00 38.38 2.57
210 219 2.876550 GTCCTCAAAGGTAACAAGCGTT 59.123 45.455 0.00 0.00 36.53 4.84
304 313 4.200092 GACTTCCAAACCTTCACAGACTT 58.800 43.478 0.00 0.00 0.00 3.01
347 356 0.456221 ACACAGACCTCGCCTAATCG 59.544 55.000 0.00 0.00 0.00 3.34
414 423 1.066358 GTTGGAGCGGCTAGGTAGTTT 60.066 52.381 0.60 0.00 0.00 2.66
417 427 1.327690 TGGTTGGAGCGGCTAGGTAG 61.328 60.000 0.60 0.00 0.00 3.18
439 449 3.366985 CCAACTGCTGTGATAGTCGTACA 60.367 47.826 0.00 0.00 0.00 2.90
509 519 4.453480 TGAGGAAATGAAAGGGTTGAGT 57.547 40.909 0.00 0.00 0.00 3.41
553 563 6.206634 TCAGTCAAAGTCTTCAAACAACAACT 59.793 34.615 0.00 0.00 0.00 3.16
557 567 6.743172 GTCTTCAGTCAAAGTCTTCAAACAAC 59.257 38.462 0.00 0.00 0.00 3.32
630 640 6.994221 AGTAGCGTGTAAATAGGATAAGCAT 58.006 36.000 0.00 0.00 0.00 3.79
689 700 4.578871 TGCATAACAGAACAGTAGCACAT 58.421 39.130 0.00 0.00 0.00 3.21
718 729 2.493713 AGCAGCGGAATAAGTACTCG 57.506 50.000 0.00 0.00 0.00 4.18
870 887 1.305201 GAAGAACAGCACCCGTTCAA 58.695 50.000 5.89 0.00 44.22 2.69
872 889 0.868406 CTGAAGAACAGCACCCGTTC 59.132 55.000 0.00 0.00 42.52 3.95
1001 1018 2.185867 GACGATTGTAGCCCGCCA 59.814 61.111 0.00 0.00 0.00 5.69
1010 1027 9.214957 TGTCAAAGTTAATAATGAGACGATTGT 57.785 29.630 0.00 0.00 0.00 2.71
1224 1241 6.045106 ACAATTTGTTCCCTAGGTTCCTCTAA 59.955 38.462 8.29 0.00 0.00 2.10
1312 1330 3.244976 GTTTTTGATTGATCAGGCGTGG 58.755 45.455 6.56 0.00 38.19 4.94
1316 1334 6.401796 GCTGAAATGTTTTTGATTGATCAGGC 60.402 38.462 0.00 0.00 38.19 4.85
1382 1400 0.739462 CCGGTTGCGTATGCTCTGAA 60.739 55.000 8.69 0.00 43.34 3.02
1408 1426 3.947196 GACCAACATCAATGCATGTAGGA 59.053 43.478 0.00 0.00 35.87 2.94
1426 1444 0.603065 CAGTCACGTCCATCTGACCA 59.397 55.000 0.00 0.00 41.18 4.02
1475 1493 2.396590 GGATTTAGCTCCGACAACCA 57.603 50.000 0.00 0.00 0.00 3.67
1512 1530 4.640690 ACCACCAGCTCGGGACCT 62.641 66.667 0.00 0.00 40.22 3.85
1517 1535 2.046892 CCAAGACCACCAGCTCGG 60.047 66.667 1.16 1.16 42.50 4.63
1518 1536 1.888436 TAGCCAAGACCACCAGCTCG 61.888 60.000 0.00 0.00 35.03 5.03
1669 1697 7.078011 AGGAAAATCTTTTAGACTCATTCGC 57.922 36.000 0.00 0.00 0.00 4.70
1695 1723 1.465200 GCCGAGGGGTCTAGTCCATC 61.465 65.000 8.34 8.53 34.97 3.51
1704 1732 1.071857 CCCTAAATAAGCCGAGGGGTC 59.928 57.143 0.00 0.00 44.41 4.46
1787 1815 0.041312 ACACGCTTCAACGCATGTTC 60.041 50.000 0.00 0.00 35.72 3.18
1802 1830 0.242825 TCCCGAAGACTTAGCACACG 59.757 55.000 0.00 0.00 0.00 4.49
1819 1847 3.370633 GGGGTACTCAAGATGGAAAGTCC 60.371 52.174 0.00 0.00 36.96 3.85
1822 1850 4.265073 CTTGGGGTACTCAAGATGGAAAG 58.735 47.826 18.22 0.00 42.94 2.62
1886 1914 3.713288 TGACAGAAAACGTGACCTACTG 58.287 45.455 0.00 0.00 0.00 2.74
1924 1952 8.768955 ACTATCTTGATTCTGTCATAAAATCGC 58.231 33.333 0.00 0.00 36.54 4.58
1950 1978 4.711846 ACTTCTATGACAGCACAGGTATGA 59.288 41.667 0.00 0.00 0.00 2.15
2022 2050 2.248431 GACGCGCCATTTATCGGC 59.752 61.111 5.73 0.00 46.62 5.54
2023 2051 2.235016 ACGACGCGCCATTTATCGG 61.235 57.895 5.73 0.00 37.11 4.18
2024 2052 1.084290 CACGACGCGCCATTTATCG 60.084 57.895 5.73 8.98 38.71 2.92
2025 2053 1.149361 TCCACGACGCGCCATTTATC 61.149 55.000 5.73 0.00 0.00 1.75
2026 2054 0.741574 TTCCACGACGCGCCATTTAT 60.742 50.000 5.73 0.00 0.00 1.40
2027 2055 1.355796 CTTCCACGACGCGCCATTTA 61.356 55.000 5.73 0.00 0.00 1.40
2028 2056 2.666862 TTCCACGACGCGCCATTT 60.667 55.556 5.73 0.00 0.00 2.32
2029 2057 3.118454 CTTCCACGACGCGCCATT 61.118 61.111 5.73 0.00 0.00 3.16
2030 2058 4.373116 ACTTCCACGACGCGCCAT 62.373 61.111 5.73 0.00 0.00 4.40
2034 2062 2.480426 GAAAGCACTTCCACGACGCG 62.480 60.000 3.53 3.53 0.00 6.01
2035 2063 1.204312 GAAAGCACTTCCACGACGC 59.796 57.895 0.00 0.00 0.00 5.19
2036 2064 1.213094 ACGAAAGCACTTCCACGACG 61.213 55.000 0.00 0.00 0.00 5.12
2037 2065 0.507358 GACGAAAGCACTTCCACGAC 59.493 55.000 0.00 0.00 0.00 4.34
2038 2066 0.103390 TGACGAAAGCACTTCCACGA 59.897 50.000 0.00 0.00 0.00 4.35
2039 2067 0.934496 TTGACGAAAGCACTTCCACG 59.066 50.000 0.00 0.00 0.00 4.94
2040 2068 1.264288 CCTTGACGAAAGCACTTCCAC 59.736 52.381 0.00 0.00 34.24 4.02
2041 2069 1.593196 CCTTGACGAAAGCACTTCCA 58.407 50.000 0.00 0.00 34.24 3.53
2042 2070 0.875059 CCCTTGACGAAAGCACTTCC 59.125 55.000 0.00 0.00 34.24 3.46
2043 2071 1.594331 ACCCTTGACGAAAGCACTTC 58.406 50.000 0.00 0.00 34.24 3.01
2044 2072 2.876550 GTTACCCTTGACGAAAGCACTT 59.123 45.455 0.00 0.00 34.24 3.16
2045 2073 2.490991 GTTACCCTTGACGAAAGCACT 58.509 47.619 0.00 0.00 34.24 4.40
2046 2074 1.534163 GGTTACCCTTGACGAAAGCAC 59.466 52.381 0.00 0.00 34.24 4.40
2047 2075 1.874739 CGGTTACCCTTGACGAAAGCA 60.875 52.381 0.00 0.00 34.24 3.91
2048 2076 0.794473 CGGTTACCCTTGACGAAAGC 59.206 55.000 0.00 0.00 34.24 3.51
2049 2077 2.064014 GTCGGTTACCCTTGACGAAAG 58.936 52.381 0.00 0.00 35.17 2.62
2050 2078 1.411977 TGTCGGTTACCCTTGACGAAA 59.588 47.619 0.00 0.00 35.17 3.46
2051 2079 1.039068 TGTCGGTTACCCTTGACGAA 58.961 50.000 0.00 0.00 35.17 3.85
2052 2080 0.314935 GTGTCGGTTACCCTTGACGA 59.685 55.000 0.00 0.00 34.11 4.20
2053 2081 0.032403 TGTGTCGGTTACCCTTGACG 59.968 55.000 0.00 0.00 34.11 4.35
2054 2082 2.073816 CATGTGTCGGTTACCCTTGAC 58.926 52.381 0.00 0.00 0.00 3.18
2055 2083 1.002659 CCATGTGTCGGTTACCCTTGA 59.997 52.381 0.00 0.00 0.00 3.02
2056 2084 1.448985 CCATGTGTCGGTTACCCTTG 58.551 55.000 0.00 0.00 0.00 3.61
2057 2085 0.322187 GCCATGTGTCGGTTACCCTT 60.322 55.000 0.00 0.00 0.00 3.95
2058 2086 1.298667 GCCATGTGTCGGTTACCCT 59.701 57.895 0.00 0.00 0.00 4.34
2059 2087 0.393808 ATGCCATGTGTCGGTTACCC 60.394 55.000 0.00 0.00 0.00 3.69
2060 2088 1.014352 GATGCCATGTGTCGGTTACC 58.986 55.000 0.00 0.00 0.00 2.85
2061 2089 1.014352 GGATGCCATGTGTCGGTTAC 58.986 55.000 0.00 0.00 0.00 2.50
2062 2090 0.615850 TGGATGCCATGTGTCGGTTA 59.384 50.000 0.00 0.00 0.00 2.85
2063 2091 0.034186 ATGGATGCCATGTGTCGGTT 60.034 50.000 0.00 0.00 43.39 4.44
2064 2092 0.464373 GATGGATGCCATGTGTCGGT 60.464 55.000 3.25 0.00 45.26 4.69
2065 2093 1.501337 CGATGGATGCCATGTGTCGG 61.501 60.000 3.25 0.00 45.26 4.79
2066 2094 0.811219 ACGATGGATGCCATGTGTCG 60.811 55.000 3.25 4.78 45.26 4.35
2067 2095 2.238942 TACGATGGATGCCATGTGTC 57.761 50.000 3.25 0.00 45.26 3.67
2068 2096 2.288666 GTTACGATGGATGCCATGTGT 58.711 47.619 3.25 5.12 45.26 3.72
2069 2097 1.261354 CGTTACGATGGATGCCATGTG 59.739 52.381 3.25 0.00 45.26 3.21
2070 2098 1.581934 CGTTACGATGGATGCCATGT 58.418 50.000 3.25 5.44 45.26 3.21
2071 2099 0.867746 CCGTTACGATGGATGCCATG 59.132 55.000 6.24 0.00 45.26 3.66
2073 2101 1.145156 CCCGTTACGATGGATGCCA 59.855 57.895 6.24 0.00 38.19 4.92
2074 2102 0.878961 GACCCGTTACGATGGATGCC 60.879 60.000 6.24 0.00 33.44 4.40
2075 2103 0.179094 TGACCCGTTACGATGGATGC 60.179 55.000 6.24 0.00 33.44 3.91
2076 2104 1.567504 GTGACCCGTTACGATGGATG 58.432 55.000 6.24 0.00 33.44 3.51
2077 2105 0.462789 GGTGACCCGTTACGATGGAT 59.537 55.000 6.24 0.00 33.44 3.41
2078 2106 1.892338 GGTGACCCGTTACGATGGA 59.108 57.895 6.24 0.00 33.44 3.41
2079 2107 4.507879 GGTGACCCGTTACGATGG 57.492 61.111 6.24 1.93 0.00 3.51
2089 2117 2.285977 CCAATAGCTTAACGGTGACCC 58.714 52.381 0.00 0.00 0.00 4.46
2090 2118 2.285977 CCCAATAGCTTAACGGTGACC 58.714 52.381 0.00 0.00 0.00 4.02
2091 2119 2.981898 ACCCAATAGCTTAACGGTGAC 58.018 47.619 0.00 0.00 0.00 3.67
2092 2120 3.602483 GAACCCAATAGCTTAACGGTGA 58.398 45.455 0.00 0.00 0.00 4.02
2093 2121 2.681344 GGAACCCAATAGCTTAACGGTG 59.319 50.000 0.00 0.00 0.00 4.94
2094 2122 2.678769 CGGAACCCAATAGCTTAACGGT 60.679 50.000 0.00 0.00 0.00 4.83
2095 2123 1.937899 CGGAACCCAATAGCTTAACGG 59.062 52.381 0.00 0.00 0.00 4.44
2096 2124 1.937899 CCGGAACCCAATAGCTTAACG 59.062 52.381 0.00 0.00 0.00 3.18
2097 2125 2.995283 ACCGGAACCCAATAGCTTAAC 58.005 47.619 9.46 0.00 0.00 2.01
2098 2126 3.724732 AACCGGAACCCAATAGCTTAA 57.275 42.857 9.46 0.00 0.00 1.85
2099 2127 3.349022 CAAACCGGAACCCAATAGCTTA 58.651 45.455 9.46 0.00 0.00 3.09
2100 2128 2.167662 CAAACCGGAACCCAATAGCTT 58.832 47.619 9.46 0.00 0.00 3.74
2101 2129 1.615919 CCAAACCGGAACCCAATAGCT 60.616 52.381 9.46 0.00 36.56 3.32
2102 2130 0.815095 CCAAACCGGAACCCAATAGC 59.185 55.000 9.46 0.00 36.56 2.97
2103 2131 2.500392 TCCAAACCGGAACCCAATAG 57.500 50.000 9.46 0.00 42.52 1.73
2113 2141 2.572290 GGGTTATCAGATCCAAACCGG 58.428 52.381 0.00 0.00 41.90 5.28
2114 2142 2.210116 CGGGTTATCAGATCCAAACCG 58.790 52.381 7.81 7.81 45.14 4.44
2115 2143 3.277142 ACGGGTTATCAGATCCAAACC 57.723 47.619 5.31 5.31 40.56 3.27
2116 2144 5.644636 TGTTAACGGGTTATCAGATCCAAAC 59.355 40.000 0.26 0.00 0.00 2.93
2117 2145 5.806818 TGTTAACGGGTTATCAGATCCAAA 58.193 37.500 0.26 0.00 0.00 3.28
2118 2146 5.423704 TGTTAACGGGTTATCAGATCCAA 57.576 39.130 0.26 0.00 0.00 3.53
2119 2147 4.682320 GCTGTTAACGGGTTATCAGATCCA 60.682 45.833 23.77 0.00 41.73 3.41
2120 2148 3.808174 GCTGTTAACGGGTTATCAGATCC 59.192 47.826 23.77 10.02 41.73 3.36
2121 2149 3.808174 GGCTGTTAACGGGTTATCAGATC 59.192 47.826 23.77 15.05 41.73 2.75
2122 2150 3.433173 GGGCTGTTAACGGGTTATCAGAT 60.433 47.826 23.77 0.00 41.73 2.90
2123 2151 2.093341 GGGCTGTTAACGGGTTATCAGA 60.093 50.000 23.77 0.00 41.73 3.27
2124 2152 2.285977 GGGCTGTTAACGGGTTATCAG 58.714 52.381 16.13 18.63 41.92 2.90
2125 2153 1.405797 CGGGCTGTTAACGGGTTATCA 60.406 52.381 16.13 3.20 0.00 2.15
2126 2154 1.292992 CGGGCTGTTAACGGGTTATC 58.707 55.000 16.13 0.00 0.00 1.75
2127 2155 0.107557 CCGGGCTGTTAACGGGTTAT 60.108 55.000 16.13 0.00 43.69 1.89
2128 2156 1.296068 CCGGGCTGTTAACGGGTTA 59.704 57.895 16.13 0.00 43.69 2.85
2129 2157 2.032987 CCGGGCTGTTAACGGGTT 59.967 61.111 16.13 0.00 43.69 4.11
2133 2161 0.675522 ATTGGTCCGGGCTGTTAACG 60.676 55.000 5.77 0.00 0.00 3.18
2134 2162 0.808755 CATTGGTCCGGGCTGTTAAC 59.191 55.000 5.77 0.00 0.00 2.01
2135 2163 0.322997 CCATTGGTCCGGGCTGTTAA 60.323 55.000 5.77 0.00 0.00 2.01
2136 2164 1.301623 CCATTGGTCCGGGCTGTTA 59.698 57.895 5.77 0.00 0.00 2.41
2137 2165 2.035626 CCATTGGTCCGGGCTGTT 59.964 61.111 5.77 0.00 0.00 3.16
2138 2166 4.047125 CCCATTGGTCCGGGCTGT 62.047 66.667 5.77 0.00 35.09 4.40
2139 2167 4.820744 CCCCATTGGTCCGGGCTG 62.821 72.222 5.77 0.00 41.57 4.85
2141 2169 2.871795 AAATCCCCATTGGTCCGGGC 62.872 60.000 0.00 0.00 41.57 6.13
2142 2170 0.325203 AAAATCCCCATTGGTCCGGG 60.325 55.000 0.00 0.00 42.67 5.73
2143 2171 1.111277 GAAAATCCCCATTGGTCCGG 58.889 55.000 0.00 0.00 34.77 5.14
2144 2172 1.111277 GGAAAATCCCCATTGGTCCG 58.889 55.000 1.20 0.00 34.77 4.79
2145 2173 1.831106 GTGGAAAATCCCCATTGGTCC 59.169 52.381 1.20 1.47 35.03 4.46
2146 2174 1.476488 CGTGGAAAATCCCCATTGGTC 59.524 52.381 1.20 0.00 35.03 4.02
2147 2175 1.203125 ACGTGGAAAATCCCCATTGGT 60.203 47.619 1.20 0.00 35.03 3.67
2148 2176 1.204467 CACGTGGAAAATCCCCATTGG 59.796 52.381 7.95 0.00 35.03 3.16
2149 2177 1.892474 ACACGTGGAAAATCCCCATTG 59.108 47.619 21.57 0.00 35.03 2.82
2150 2178 2.302587 ACACGTGGAAAATCCCCATT 57.697 45.000 21.57 0.00 35.03 3.16
2151 2179 3.443145 TTACACGTGGAAAATCCCCAT 57.557 42.857 21.57 0.00 35.03 4.00
2152 2180 2.953284 TTACACGTGGAAAATCCCCA 57.047 45.000 21.57 0.00 35.03 4.96
2153 2181 4.794278 ATTTTACACGTGGAAAATCCCC 57.206 40.909 35.26 0.00 35.03 4.81
2154 2182 7.540299 TGATAATTTTACACGTGGAAAATCCC 58.460 34.615 38.49 30.23 34.86 3.85
2155 2183 8.973835 TTGATAATTTTACACGTGGAAAATCC 57.026 30.769 38.49 30.48 34.86 3.01
2157 2185 9.364989 CCATTGATAATTTTACACGTGGAAAAT 57.635 29.630 35.26 35.26 36.94 1.82
2158 2186 7.329717 GCCATTGATAATTTTACACGTGGAAAA 59.670 33.333 34.26 34.26 0.00 2.29
2159 2187 6.809196 GCCATTGATAATTTTACACGTGGAAA 59.191 34.615 21.99 21.99 0.00 3.13
2160 2188 6.151985 AGCCATTGATAATTTTACACGTGGAA 59.848 34.615 21.57 16.11 0.00 3.53
2161 2189 5.650266 AGCCATTGATAATTTTACACGTGGA 59.350 36.000 21.57 9.00 0.00 4.02
2162 2190 5.890334 AGCCATTGATAATTTTACACGTGG 58.110 37.500 21.57 1.66 0.00 4.94
2163 2191 7.915508 TCTAGCCATTGATAATTTTACACGTG 58.084 34.615 15.48 15.48 0.00 4.49
2164 2192 7.226720 CCTCTAGCCATTGATAATTTTACACGT 59.773 37.037 0.00 0.00 0.00 4.49
2165 2193 7.441157 TCCTCTAGCCATTGATAATTTTACACG 59.559 37.037 0.00 0.00 0.00 4.49
2166 2194 8.677148 TCCTCTAGCCATTGATAATTTTACAC 57.323 34.615 0.00 0.00 0.00 2.90
2167 2195 9.120538 GTTCCTCTAGCCATTGATAATTTTACA 57.879 33.333 0.00 0.00 0.00 2.41
2168 2196 8.568794 GGTTCCTCTAGCCATTGATAATTTTAC 58.431 37.037 0.00 0.00 0.00 2.01
2169 2197 8.278639 TGGTTCCTCTAGCCATTGATAATTTTA 58.721 33.333 0.00 0.00 32.74 1.52
2170 2198 7.068716 GTGGTTCCTCTAGCCATTGATAATTTT 59.931 37.037 0.00 0.00 41.02 1.82
2171 2199 6.547510 GTGGTTCCTCTAGCCATTGATAATTT 59.452 38.462 0.00 0.00 41.02 1.82
2172 2200 6.064717 GTGGTTCCTCTAGCCATTGATAATT 58.935 40.000 0.00 0.00 41.02 1.40
2173 2201 5.625150 GTGGTTCCTCTAGCCATTGATAAT 58.375 41.667 0.00 0.00 41.02 1.28
2174 2202 4.442893 CGTGGTTCCTCTAGCCATTGATAA 60.443 45.833 0.00 0.00 41.02 1.75
2175 2203 3.069586 CGTGGTTCCTCTAGCCATTGATA 59.930 47.826 0.00 0.00 41.02 2.15
2176 2204 2.158900 CGTGGTTCCTCTAGCCATTGAT 60.159 50.000 0.00 0.00 41.02 2.57
2177 2205 1.207089 CGTGGTTCCTCTAGCCATTGA 59.793 52.381 0.00 0.00 41.02 2.57
2178 2206 1.066143 ACGTGGTTCCTCTAGCCATTG 60.066 52.381 0.00 0.00 41.02 2.82
2179 2207 1.066143 CACGTGGTTCCTCTAGCCATT 60.066 52.381 7.95 0.00 41.02 3.16
2180 2208 0.537188 CACGTGGTTCCTCTAGCCAT 59.463 55.000 7.95 0.00 41.02 4.40
2181 2209 0.830444 ACACGTGGTTCCTCTAGCCA 60.830 55.000 21.57 0.00 35.85 4.75
2182 2210 0.108756 GACACGTGGTTCCTCTAGCC 60.109 60.000 21.57 0.00 0.00 3.93
2183 2211 0.456312 CGACACGTGGTTCCTCTAGC 60.456 60.000 21.57 0.00 0.00 3.42
2184 2212 0.170561 CCGACACGTGGTTCCTCTAG 59.829 60.000 21.57 0.00 0.00 2.43
2185 2213 1.870055 GCCGACACGTGGTTCCTCTA 61.870 60.000 21.57 0.00 0.00 2.43
2186 2214 3.048602 CCGACACGTGGTTCCTCT 58.951 61.111 21.57 0.00 0.00 3.69
2187 2215 2.737376 GCCGACACGTGGTTCCTC 60.737 66.667 21.57 6.77 0.00 3.71
2188 2216 3.222354 GAGCCGACACGTGGTTCCT 62.222 63.158 21.57 10.48 31.17 3.36
2189 2217 2.737376 GAGCCGACACGTGGTTCC 60.737 66.667 21.57 5.48 31.17 3.62
2190 2218 2.022129 CTGAGCCGACACGTGGTTC 61.022 63.158 21.57 10.33 37.25 3.62
2191 2219 2.029073 CTGAGCCGACACGTGGTT 59.971 61.111 21.57 0.00 0.00 3.67
2192 2220 4.664677 GCTGAGCCGACACGTGGT 62.665 66.667 21.57 5.35 0.00 4.16
2195 2223 4.280494 AACGCTGAGCCGACACGT 62.280 61.111 0.00 0.00 38.88 4.49
2196 2224 3.767230 CAACGCTGAGCCGACACG 61.767 66.667 0.00 0.00 0.00 4.49
2197 2225 3.414700 CCAACGCTGAGCCGACAC 61.415 66.667 0.00 0.00 0.00 3.67
2198 2226 4.680237 CCCAACGCTGAGCCGACA 62.680 66.667 0.00 0.00 0.00 4.35
2199 2227 4.373116 TCCCAACGCTGAGCCGAC 62.373 66.667 0.00 0.00 0.00 4.79
2200 2228 4.373116 GTCCCAACGCTGAGCCGA 62.373 66.667 0.00 0.00 0.00 5.54
2201 2229 4.680237 TGTCCCAACGCTGAGCCG 62.680 66.667 0.00 0.00 0.00 5.52
2202 2230 2.527951 ATCTGTCCCAACGCTGAGCC 62.528 60.000 0.00 0.00 0.00 4.70
2203 2231 0.175760 TATCTGTCCCAACGCTGAGC 59.824 55.000 0.00 0.00 0.00 4.26
2204 2232 2.101415 TGATATCTGTCCCAACGCTGAG 59.899 50.000 3.98 0.00 0.00 3.35
2205 2233 2.107366 TGATATCTGTCCCAACGCTGA 58.893 47.619 3.98 0.00 0.00 4.26
2206 2234 2.602257 TGATATCTGTCCCAACGCTG 57.398 50.000 3.98 0.00 0.00 5.18
2207 2235 2.037772 GGATGATATCTGTCCCAACGCT 59.962 50.000 13.66 0.00 0.00 5.07
2208 2236 2.224281 TGGATGATATCTGTCCCAACGC 60.224 50.000 18.93 1.59 0.00 4.84
2209 2237 3.070159 AGTGGATGATATCTGTCCCAACG 59.930 47.826 18.93 0.00 0.00 4.10
2210 2238 4.101585 TGAGTGGATGATATCTGTCCCAAC 59.898 45.833 18.93 13.62 0.00 3.77
2211 2239 4.297768 TGAGTGGATGATATCTGTCCCAA 58.702 43.478 18.93 5.08 0.00 4.12
2212 2240 3.927476 TGAGTGGATGATATCTGTCCCA 58.073 45.455 18.93 11.45 0.00 4.37
2213 2241 5.243981 CAATGAGTGGATGATATCTGTCCC 58.756 45.833 18.93 12.87 0.00 4.46
2228 2256 1.450312 GCCTCCCGTCCAATGAGTG 60.450 63.158 0.00 0.00 0.00 3.51
2229 2257 2.990479 GCCTCCCGTCCAATGAGT 59.010 61.111 0.00 0.00 0.00 3.41
2230 2258 2.202932 CGCCTCCCGTCCAATGAG 60.203 66.667 0.00 0.00 0.00 2.90
2231 2259 4.467084 GCGCCTCCCGTCCAATGA 62.467 66.667 0.00 0.00 39.71 2.57
2235 2263 4.853142 ATAGGCGCCTCCCGTCCA 62.853 66.667 36.73 14.96 44.17 4.02
2236 2264 4.301027 CATAGGCGCCTCCCGTCC 62.301 72.222 36.73 0.00 44.17 4.79
2237 2265 1.248785 TATCATAGGCGCCTCCCGTC 61.249 60.000 36.73 0.00 43.21 4.79
2238 2266 1.228769 TATCATAGGCGCCTCCCGT 60.229 57.895 36.73 20.23 39.71 5.28
2239 2267 1.215647 GTATCATAGGCGCCTCCCG 59.784 63.158 36.73 22.51 40.75 5.14
2240 2268 1.215647 CGTATCATAGGCGCCTCCC 59.784 63.158 36.73 14.14 34.51 4.30
2241 2269 0.109226 GACGTATCATAGGCGCCTCC 60.109 60.000 36.73 13.77 0.00 4.30
2242 2270 0.454620 CGACGTATCATAGGCGCCTC 60.455 60.000 36.73 17.10 0.00 4.70
2243 2271 0.887836 TCGACGTATCATAGGCGCCT 60.888 55.000 34.85 34.85 0.00 5.52
2244 2272 0.728466 GTCGACGTATCATAGGCGCC 60.728 60.000 21.89 21.89 0.00 6.53
2245 2273 0.040692 TGTCGACGTATCATAGGCGC 60.041 55.000 11.62 0.00 0.00 6.53
2246 2274 1.003223 TGTGTCGACGTATCATAGGCG 60.003 52.381 11.62 0.00 0.00 5.52
2247 2275 2.768833 TGTGTCGACGTATCATAGGC 57.231 50.000 11.62 0.00 0.00 3.93
2248 2276 3.565516 CCATGTGTCGACGTATCATAGG 58.434 50.000 11.62 11.84 0.00 2.57
2249 2277 2.980476 GCCATGTGTCGACGTATCATAG 59.020 50.000 11.62 7.34 0.00 2.23
2250 2278 2.359531 TGCCATGTGTCGACGTATCATA 59.640 45.455 11.62 0.00 0.00 2.15
2251 2279 1.136110 TGCCATGTGTCGACGTATCAT 59.864 47.619 11.62 9.83 0.00 2.45
2252 2280 0.528470 TGCCATGTGTCGACGTATCA 59.472 50.000 11.62 7.93 0.00 2.15
2253 2281 0.921347 GTGCCATGTGTCGACGTATC 59.079 55.000 11.62 2.18 0.00 2.24
2254 2282 0.800683 CGTGCCATGTGTCGACGTAT 60.801 55.000 11.62 4.77 0.00 3.06
2255 2283 1.443025 CGTGCCATGTGTCGACGTA 60.443 57.895 11.62 2.21 0.00 3.57
2256 2284 2.733218 CGTGCCATGTGTCGACGT 60.733 61.111 11.62 0.00 0.00 4.34
2257 2285 3.478394 CCGTGCCATGTGTCGACG 61.478 66.667 11.62 0.00 0.00 5.12
2258 2286 3.788766 GCCGTGCCATGTGTCGAC 61.789 66.667 9.11 9.11 0.00 4.20


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

AutoCloner maintained by Alex Coulton.