Multiple sequence alignment - TraesCS3A01G193300

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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 TraesCS3A01G193300 chr3A 100.000 2459 0 0 1 2459 261386982 261384524 0.000000e+00 4542.0
1 TraesCS3A01G193300 chr3A 89.944 179 13 2 275 449 575781688 575781865 2.460000e-55 226.0
2 TraesCS3A01G193300 chr2A 91.453 1404 88 13 275 1650 326260558 326261957 0.000000e+00 1899.0
3 TraesCS3A01G193300 chr2A 95.652 276 11 1 1 276 326259830 326260104 2.240000e-120 442.0
4 TraesCS3A01G193300 chr2A 91.633 251 18 3 1718 1968 326261959 326262206 6.510000e-91 344.0
5 TraesCS3A01G193300 chr2A 86.243 189 25 1 1969 2157 133352822 133353009 1.150000e-48 204.0
6 TraesCS3A01G193300 chr2A 91.453 117 6 3 1856 1971 133352679 133352792 9.100000e-35 158.0
7 TraesCS3A01G193300 chr2A 87.097 124 13 2 3 124 399643988 399643866 1.190000e-28 137.0
8 TraesCS3A01G193300 chr7D 92.589 1120 52 6 275 1364 351661918 351660800 0.000000e+00 1580.0
9 TraesCS3A01G193300 chr7D 90.998 611 48 5 1360 1968 351659839 351659234 0.000000e+00 817.0
10 TraesCS3A01G193300 chr7D 94.975 199 9 1 1 199 351662623 351662426 6.600000e-81 311.0
11 TraesCS3A01G193300 chr7D 89.560 182 17 2 1970 2151 351659200 351659021 1.900000e-56 230.0
12 TraesCS3A01G193300 chr7D 86.740 181 21 3 2092 2270 400227343 400227164 5.360000e-47 198.0
13 TraesCS3A01G193300 chr7D 85.625 160 19 2 2111 2269 488113393 488113237 5.440000e-37 165.0
14 TraesCS3A01G193300 chr7D 96.154 52 2 0 226 277 351662421 351662370 4.360000e-13 86.1
15 TraesCS3A01G193300 chr3B 90.568 1092 52 13 275 1339 182738445 182739512 0.000000e+00 1399.0
16 TraesCS3A01G193300 chr3B 88.764 267 14 6 1545 1810 182739513 182739764 1.840000e-81 313.0
17 TraesCS3A01G193300 chr3B 92.742 124 9 0 1 124 170806463 170806586 1.940000e-41 180.0
18 TraesCS3A01G193300 chr3B 88.462 104 7 3 1865 1968 182739767 182739865 1.190000e-23 121.0
19 TraesCS3A01G193300 chr6B 90.210 1093 56 11 275 1339 420917194 420918263 0.000000e+00 1378.0
20 TraesCS3A01G193300 chr6B 88.889 270 14 5 1545 1813 420918264 420918518 3.950000e-83 318.0
21 TraesCS3A01G193300 chr6B 91.620 179 10 2 275 449 430582412 430582235 2.440000e-60 243.0
22 TraesCS3A01G193300 chr6B 89.381 113 12 0 3 115 131264248 131264136 2.550000e-30 143.0
23 TraesCS3A01G193300 chr6B 88.235 119 6 5 1850 1968 420918514 420918624 4.270000e-28 135.0
24 TraesCS3A01G193300 chr1B 90.654 963 56 11 275 1217 590409122 590410070 0.000000e+00 1249.0
25 TraesCS3A01G193300 chr1B 89.791 911 43 10 275 1158 458705669 458704782 0.000000e+00 1122.0
26 TraesCS3A01G193300 chr1B 88.961 462 29 9 1218 1661 590414857 590415314 3.570000e-153 551.0
27 TraesCS3A01G193300 chr1B 93.841 276 16 1 1 276 590408393 590408667 4.890000e-112 414.0
28 TraesCS3A01G193300 chr1B 88.192 271 15 4 1545 1813 458704727 458704472 8.540000e-80 307.0
29 TraesCS3A01G193300 chr1B 92.241 116 7 2 1661 1776 590416680 590416793 1.960000e-36 163.0
30 TraesCS3A01G193300 chr1B 89.423 104 6 3 1865 1968 458704468 458704370 2.570000e-25 126.0
31 TraesCS3A01G193300 chr5B 91.345 855 67 3 639 1489 245725147 245725998 0.000000e+00 1162.0
32 TraesCS3A01G193300 chr5B 86.875 160 19 2 2153 2311 681293773 681293615 6.990000e-41 178.0
33 TraesCS3A01G193300 chr7A 91.963 759 29 4 854 1608 217736906 217736176 0.000000e+00 1035.0
34 TraesCS3A01G193300 chr7A 94.631 447 24 0 412 858 217746153 217745707 0.000000e+00 693.0
35 TraesCS3A01G193300 chr7A 95.366 410 12 4 1564 1971 299396363 299395959 0.000000e+00 645.0
36 TraesCS3A01G193300 chr7A 94.390 410 13 7 1564 1970 217736178 217735776 2.690000e-174 621.0
37 TraesCS3A01G193300 chr7A 96.000 300 11 1 1310 1608 299396660 299396361 1.020000e-133 486.0
38 TraesCS3A01G193300 chr7A 92.857 182 13 0 1969 2150 217735745 217735564 5.210000e-67 265.0
39 TraesCS3A01G193300 chr7A 91.176 170 15 0 1972 2141 299395926 299395757 5.290000e-57 231.0
40 TraesCS3A01G193300 chr7A 87.195 164 19 2 2166 2328 263171460 263171298 4.180000e-43 185.0
41 TraesCS3A01G193300 chr2B 87.121 264 32 2 15 276 784624782 784624519 5.140000e-77 298.0
42 TraesCS3A01G193300 chr2B 71.154 468 125 9 1031 1492 77533615 77534078 9.300000e-20 108.0
43 TraesCS3A01G193300 chr2B 95.745 47 2 0 1710 1756 784624372 784624326 2.620000e-10 76.8
44 TraesCS3A01G193300 chr2D 86.878 221 28 1 56 276 396181229 396181448 1.890000e-61 246.0
45 TraesCS3A01G193300 chr2D 73.048 397 100 7 1097 1491 612522385 612521994 1.530000e-27 134.0
46 TraesCS3A01G193300 chr4D 85.789 190 13 10 275 453 159612455 159612269 3.230000e-44 189.0
47 TraesCS3A01G193300 chr6D 87.421 159 18 2 2112 2269 291663634 291663791 5.400000e-42 182.0
48 TraesCS3A01G193300 chr1D 87.662 154 18 1 2150 2302 202311108 202311261 6.990000e-41 178.0
49 TraesCS3A01G193300 chr1D 85.714 161 17 4 2113 2270 50885268 50885425 5.440000e-37 165.0
50 TraesCS3A01G193300 chr1D 72.775 382 102 2 1110 1490 11671482 11671102 7.140000e-26 128.0
51 TraesCS3A01G193300 chr1D 95.455 66 3 0 2313 2378 275719115 275719180 3.340000e-19 106.0
52 TraesCS3A01G193300 chr5D 85.806 155 15 5 2112 2263 22526996 22527146 9.100000e-35 158.0
53 TraesCS3A01G193300 chr3D 84.211 171 17 7 2107 2270 141341909 141342076 9.100000e-35 158.0
54 TraesCS3A01G193300 chr4A 88.525 122 8 2 1 122 619157280 619157165 2.550000e-30 143.0
55 TraesCS3A01G193300 chrUn 84.247 146 18 1 1487 1632 231783285 231783145 1.190000e-28 137.0
56 TraesCS3A01G193300 chrUn 84.247 146 18 1 1487 1632 231799919 231799779 1.190000e-28 137.0
57 TraesCS3A01G193300 chrUn 95.161 62 3 0 1695 1756 231782947 231782886 5.600000e-17 99.0
58 TraesCS3A01G193300 chrUn 95.161 62 3 0 1695 1756 231799581 231799520 5.600000e-17 99.0
59 TraesCS3A01G193300 chrUn 95.161 62 3 0 1695 1756 238720448 238720387 5.600000e-17 99.0
60 TraesCS3A01G193300 chrUn 86.207 87 8 4 2373 2459 306640351 306640433 9.360000e-15 91.6
61 TraesCS3A01G193300 chrUn 95.238 42 2 0 2347 2388 306640311 306640352 1.580000e-07 67.6
62 TraesCS3A01G193300 chr7B 82.895 152 9 6 2325 2459 54215910 54216061 1.190000e-23 121.0


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 TraesCS3A01G193300 chr3A 261384524 261386982 2458 True 4542.000000 4542 100.000000 1 2459 1 chr3A.!!$R1 2458
1 TraesCS3A01G193300 chr2A 326259830 326262206 2376 False 895.000000 1899 92.912667 1 1968 3 chr2A.!!$F2 1967
2 TraesCS3A01G193300 chr7D 351659021 351662623 3602 True 604.820000 1580 92.855200 1 2151 5 chr7D.!!$R3 2150
3 TraesCS3A01G193300 chr3B 182738445 182739865 1420 False 611.000000 1399 89.264667 275 1968 3 chr3B.!!$F2 1693
4 TraesCS3A01G193300 chr6B 420917194 420918624 1430 False 610.333333 1378 89.111333 275 1968 3 chr6B.!!$F1 1693
5 TraesCS3A01G193300 chr1B 590408393 590410070 1677 False 831.500000 1249 92.247500 1 1217 2 chr1B.!!$F1 1216
6 TraesCS3A01G193300 chr1B 458704370 458705669 1299 True 518.333333 1122 89.135333 275 1968 3 chr1B.!!$R1 1693
7 TraesCS3A01G193300 chr1B 590414857 590416793 1936 False 357.000000 551 90.601000 1218 1776 2 chr1B.!!$F2 558
8 TraesCS3A01G193300 chr5B 245725147 245725998 851 False 1162.000000 1162 91.345000 639 1489 1 chr5B.!!$F1 850
9 TraesCS3A01G193300 chr7A 217735564 217736906 1342 True 640.333333 1035 93.070000 854 2150 3 chr7A.!!$R3 1296
10 TraesCS3A01G193300 chr7A 299395757 299396660 903 True 454.000000 645 94.180667 1310 2141 3 chr7A.!!$R4 831

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
85 86 0.974383 AGGACGTGTAAACTGGGAGG 59.026 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 4972 0.107654 GTTTCCAGGGGATCTGTCCG 60.108 60.0 0.0 0.0 46.09 4.79 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
37 38 5.978919 CAGCAGAGCAAATGTGAAAAAGTTA 59.021 36.000 0.00 0.00 0.00 2.24
77 78 5.462530 TTGAGATTCAGAGGACGTGTAAA 57.537 39.130 0.00 0.00 0.00 2.01
85 86 0.974383 AGGACGTGTAAACTGGGAGG 59.026 55.000 0.00 0.00 0.00 4.30
94 95 3.513750 AACTGGGAGGTGGCTTGCC 62.514 63.158 4.43 4.43 0.00 4.52
95 96 3.970410 CTGGGAGGTGGCTTGCCA 61.970 66.667 10.65 10.65 34.65 4.92
96 97 3.267233 TGGGAGGTGGCTTGCCAT 61.267 61.111 17.86 2.22 30.44 4.40
97 98 1.925285 CTGGGAGGTGGCTTGCCATA 61.925 60.000 17.86 0.00 35.38 2.74
289 746 9.365906 AGTGCAATATATTCCATACAATCCAAA 57.634 29.630 0.00 0.00 0.00 3.28
449 907 9.520515 TTCTAGAACTTTTTATGCCTGAAAGAT 57.479 29.630 0.00 0.00 34.07 2.40
539 1016 6.162777 TGATTTTAGTGCAGTTAATTTGCCC 58.837 36.000 0.00 1.93 40.81 5.36
701 1180 4.505217 GCAACGATGGCGAGCACG 62.505 66.667 0.00 0.00 41.64 5.34
817 1299 1.099879 ATCCATCGCTTTGCTCTGGC 61.100 55.000 0.00 0.00 39.26 4.85
828 1310 2.425592 CTCTGGCGTTGGTGGACA 59.574 61.111 0.00 0.00 0.00 4.02
996 1482 6.016192 TCCAAGCAATACGGTGAAAATAAACA 60.016 34.615 0.00 0.00 0.00 2.83
1055 1541 0.033208 TGGGGCCTAATTTGCAGAGG 60.033 55.000 0.84 0.00 0.00 3.69
1236 1722 4.992381 AGCAATGAACTCAAACGACTAC 57.008 40.909 0.00 0.00 0.00 2.73
1305 1800 1.186200 GGACCCTTTTCATTGAGGCC 58.814 55.000 0.00 0.00 0.00 5.19
1331 1826 1.475280 GGTGTATGTGCCGAGACAGTA 59.525 52.381 0.00 0.00 0.00 2.74
1340 1842 3.068307 GTGCCGAGACAGTATAATGGACT 59.932 47.826 5.03 3.72 0.00 3.85
1419 2886 3.194755 GGTTCACCAATTACCCCAATGAC 59.805 47.826 0.00 0.00 35.64 3.06
1595 3156 3.931907 TCAAGTAGGCAGCCATGTAAT 57.068 42.857 15.80 0.00 0.00 1.89
1756 4705 9.715121 TGAATTCACGGTAATTTAGTTACTCTT 57.285 29.630 3.38 0.00 41.94 2.85
1930 4892 2.225491 CACGTGTCCTTACAAACATGGG 59.775 50.000 7.58 0.00 37.36 4.00
2044 5038 3.309410 CCTCCAGGGAAAAAGATCCACAT 60.309 47.826 0.00 0.00 41.55 3.21
2047 5041 3.094572 CAGGGAAAAAGATCCACATGCT 58.905 45.455 0.00 0.00 41.55 3.79
2064 5058 0.108424 GCTCTTCACTGGCGATGAGT 60.108 55.000 11.32 0.00 38.69 3.41
2151 5145 4.855388 ACGCACGAACATTTGTACTAGTAG 59.145 41.667 1.87 0.00 0.00 2.57
2152 5146 4.855388 CGCACGAACATTTGTACTAGTAGT 59.145 41.667 8.14 8.14 0.00 2.73
2153 5147 5.003214 CGCACGAACATTTGTACTAGTAGTC 59.997 44.000 5.96 0.00 0.00 2.59
2154 5148 6.091437 GCACGAACATTTGTACTAGTAGTCT 58.909 40.000 5.96 0.00 0.00 3.24
2155 5149 6.250951 GCACGAACATTTGTACTAGTAGTCTC 59.749 42.308 5.96 2.46 0.00 3.36
2156 5150 7.528307 CACGAACATTTGTACTAGTAGTCTCT 58.472 38.462 5.96 0.00 0.00 3.10
2157 5151 7.693120 CACGAACATTTGTACTAGTAGTCTCTC 59.307 40.741 5.96 0.00 0.00 3.20
2158 5152 7.148272 ACGAACATTTGTACTAGTAGTCTCTCC 60.148 40.741 5.96 0.00 0.00 3.71
2159 5153 7.407393 AACATTTGTACTAGTAGTCTCTCCC 57.593 40.000 5.96 0.00 0.00 4.30
2160 5154 6.733509 ACATTTGTACTAGTAGTCTCTCCCT 58.266 40.000 5.96 0.00 0.00 4.20
2161 5155 7.870027 ACATTTGTACTAGTAGTCTCTCCCTA 58.130 38.462 5.96 0.00 0.00 3.53
2162 5156 8.334734 ACATTTGTACTAGTAGTCTCTCCCTAA 58.665 37.037 5.96 0.00 0.00 2.69
2163 5157 9.357161 CATTTGTACTAGTAGTCTCTCCCTAAT 57.643 37.037 5.96 0.00 0.00 1.73
2173 5167 8.862085 AGTAGTCTCTCCCTAATAATAAAGCAC 58.138 37.037 0.00 0.00 0.00 4.40
2174 5168 6.750148 AGTCTCTCCCTAATAATAAAGCACG 58.250 40.000 0.00 0.00 0.00 5.34
2175 5169 5.927115 GTCTCTCCCTAATAATAAAGCACGG 59.073 44.000 0.00 0.00 0.00 4.94
2176 5170 5.836898 TCTCTCCCTAATAATAAAGCACGGA 59.163 40.000 0.00 0.00 0.00 4.69
2177 5171 6.497259 TCTCTCCCTAATAATAAAGCACGGAT 59.503 38.462 0.00 0.00 0.00 4.18
2178 5172 7.016268 TCTCTCCCTAATAATAAAGCACGGATT 59.984 37.037 0.00 0.00 0.00 3.01
2179 5173 6.934645 TCTCCCTAATAATAAAGCACGGATTG 59.065 38.462 0.00 0.00 0.00 2.67
2180 5174 6.833041 TCCCTAATAATAAAGCACGGATTGA 58.167 36.000 0.00 0.00 0.00 2.57
2181 5175 6.708949 TCCCTAATAATAAAGCACGGATTGAC 59.291 38.462 0.00 0.00 0.00 3.18
2182 5176 6.710744 CCCTAATAATAAAGCACGGATTGACT 59.289 38.462 0.00 0.00 0.00 3.41
2183 5177 7.228706 CCCTAATAATAAAGCACGGATTGACTT 59.771 37.037 0.00 0.00 0.00 3.01
2184 5178 8.621286 CCTAATAATAAAGCACGGATTGACTTT 58.379 33.333 0.00 0.00 36.31 2.66
2185 5179 9.438291 CTAATAATAAAGCACGGATTGACTTTG 57.562 33.333 0.00 0.00 34.97 2.77
2186 5180 5.705609 AATAAAGCACGGATTGACTTTGT 57.294 34.783 0.00 0.00 34.97 2.83
2187 5181 3.626028 AAAGCACGGATTGACTTTGTC 57.374 42.857 0.00 0.00 33.18 3.18
2188 5182 1.148310 AGCACGGATTGACTTTGTCG 58.852 50.000 0.00 0.00 34.95 4.35
2189 5183 0.165944 GCACGGATTGACTTTGTCGG 59.834 55.000 0.00 0.00 34.95 4.79
2190 5184 0.796312 CACGGATTGACTTTGTCGGG 59.204 55.000 0.00 0.00 34.95 5.14
2191 5185 0.395312 ACGGATTGACTTTGTCGGGT 59.605 50.000 0.00 0.00 34.95 5.28
2192 5186 1.202722 ACGGATTGACTTTGTCGGGTT 60.203 47.619 0.00 0.00 34.95 4.11
2193 5187 1.463444 CGGATTGACTTTGTCGGGTTC 59.537 52.381 0.00 0.00 34.95 3.62
2194 5188 2.500229 GGATTGACTTTGTCGGGTTCA 58.500 47.619 0.00 0.00 34.95 3.18
2195 5189 2.225727 GGATTGACTTTGTCGGGTTCAC 59.774 50.000 0.00 0.00 34.95 3.18
2196 5190 2.702592 TTGACTTTGTCGGGTTCACT 57.297 45.000 0.00 0.00 34.95 3.41
2197 5191 1.948104 TGACTTTGTCGGGTTCACTG 58.052 50.000 0.00 0.00 34.95 3.66
2198 5192 1.208535 TGACTTTGTCGGGTTCACTGT 59.791 47.619 0.00 0.00 34.95 3.55
2199 5193 2.285977 GACTTTGTCGGGTTCACTGTT 58.714 47.619 0.00 0.00 0.00 3.16
2200 5194 3.118702 TGACTTTGTCGGGTTCACTGTTA 60.119 43.478 0.00 0.00 34.95 2.41
2201 5195 3.200483 ACTTTGTCGGGTTCACTGTTAC 58.800 45.455 0.00 0.00 0.00 2.50
2202 5196 2.983907 TTGTCGGGTTCACTGTTACA 57.016 45.000 0.00 0.00 0.00 2.41
2203 5197 2.983907 TGTCGGGTTCACTGTTACAA 57.016 45.000 0.00 0.00 0.00 2.41
2204 5198 3.478857 TGTCGGGTTCACTGTTACAAT 57.521 42.857 0.00 0.00 0.00 2.71
2205 5199 4.603989 TGTCGGGTTCACTGTTACAATA 57.396 40.909 0.00 0.00 0.00 1.90
2206 5200 4.309099 TGTCGGGTTCACTGTTACAATAC 58.691 43.478 0.00 0.00 0.00 1.89
2207 5201 4.202233 TGTCGGGTTCACTGTTACAATACA 60.202 41.667 0.00 0.00 0.00 2.29
2208 5202 4.933400 GTCGGGTTCACTGTTACAATACAT 59.067 41.667 0.00 0.00 0.00 2.29
2209 5203 5.410439 GTCGGGTTCACTGTTACAATACATT 59.590 40.000 0.00 0.00 0.00 2.71
2210 5204 5.998981 TCGGGTTCACTGTTACAATACATTT 59.001 36.000 0.00 0.00 0.00 2.32
2211 5205 6.148150 TCGGGTTCACTGTTACAATACATTTC 59.852 38.462 0.00 0.00 0.00 2.17
2212 5206 6.148811 CGGGTTCACTGTTACAATACATTTCT 59.851 38.462 0.00 0.00 0.00 2.52
2213 5207 7.308348 CGGGTTCACTGTTACAATACATTTCTT 60.308 37.037 0.00 0.00 0.00 2.52
2214 5208 8.021396 GGGTTCACTGTTACAATACATTTCTTC 58.979 37.037 0.00 0.00 0.00 2.87
2215 5209 8.784043 GGTTCACTGTTACAATACATTTCTTCT 58.216 33.333 0.00 0.00 0.00 2.85
2216 5210 9.813080 GTTCACTGTTACAATACATTTCTTCTC 57.187 33.333 0.00 0.00 0.00 2.87
2217 5211 8.239681 TCACTGTTACAATACATTTCTTCTCG 57.760 34.615 0.00 0.00 0.00 4.04
2218 5212 7.870954 TCACTGTTACAATACATTTCTTCTCGT 59.129 33.333 0.00 0.00 0.00 4.18
2219 5213 7.952101 CACTGTTACAATACATTTCTTCTCGTG 59.048 37.037 0.00 0.00 0.00 4.35
2220 5214 7.870954 ACTGTTACAATACATTTCTTCTCGTGA 59.129 33.333 0.00 0.00 0.00 4.35
2221 5215 8.596271 TGTTACAATACATTTCTTCTCGTGAA 57.404 30.769 0.00 0.00 0.00 3.18
2222 5216 9.214957 TGTTACAATACATTTCTTCTCGTGAAT 57.785 29.630 0.00 0.00 0.00 2.57
2228 5222 9.722056 AATACATTTCTTCTCGTGAATTTATGC 57.278 29.630 0.00 0.00 0.00 3.14
2229 5223 7.383102 ACATTTCTTCTCGTGAATTTATGCT 57.617 32.000 0.00 0.00 0.00 3.79
2230 5224 7.820648 ACATTTCTTCTCGTGAATTTATGCTT 58.179 30.769 0.00 0.00 0.00 3.91
2231 5225 8.299570 ACATTTCTTCTCGTGAATTTATGCTTT 58.700 29.630 0.00 0.00 0.00 3.51
2232 5226 9.132521 CATTTCTTCTCGTGAATTTATGCTTTT 57.867 29.630 0.00 0.00 0.00 2.27
2266 5260 6.754702 ATAACATATACGCGAGGTGATACT 57.245 37.500 15.93 0.00 0.00 2.12
2267 5261 7.854557 ATAACATATACGCGAGGTGATACTA 57.145 36.000 15.93 0.00 0.00 1.82
2268 5262 6.564709 AACATATACGCGAGGTGATACTAA 57.435 37.500 15.93 0.00 0.00 2.24
2269 5263 6.754702 ACATATACGCGAGGTGATACTAAT 57.245 37.500 15.93 0.00 0.00 1.73
2270 5264 7.854557 ACATATACGCGAGGTGATACTAATA 57.145 36.000 15.93 0.00 0.00 0.98
2271 5265 8.272545 ACATATACGCGAGGTGATACTAATAA 57.727 34.615 15.93 0.00 0.00 1.40
2272 5266 8.733458 ACATATACGCGAGGTGATACTAATAAA 58.267 33.333 15.93 0.00 0.00 1.40
2273 5267 9.563898 CATATACGCGAGGTGATACTAATAAAA 57.436 33.333 15.93 0.00 0.00 1.52
2276 5270 7.781548 ACGCGAGGTGATACTAATAAAATTT 57.218 32.000 15.93 0.00 0.00 1.82
2277 5271 7.627340 ACGCGAGGTGATACTAATAAAATTTG 58.373 34.615 15.93 0.00 0.00 2.32
2278 5272 7.493320 ACGCGAGGTGATACTAATAAAATTTGA 59.507 33.333 15.93 0.00 0.00 2.69
2279 5273 8.495949 CGCGAGGTGATACTAATAAAATTTGAT 58.504 33.333 0.00 0.00 0.00 2.57
2280 5274 9.599322 GCGAGGTGATACTAATAAAATTTGATG 57.401 33.333 0.00 0.00 0.00 3.07
2281 5275 9.599322 CGAGGTGATACTAATAAAATTTGATGC 57.401 33.333 0.00 0.00 0.00 3.91
2282 5276 9.599322 GAGGTGATACTAATAAAATTTGATGCG 57.401 33.333 0.00 0.00 0.00 4.73
2283 5277 9.120538 AGGTGATACTAATAAAATTTGATGCGT 57.879 29.630 0.00 0.00 0.00 5.24
2284 5278 9.382244 GGTGATACTAATAAAATTTGATGCGTC 57.618 33.333 0.00 0.00 0.00 5.19
2285 5279 9.092322 GTGATACTAATAAAATTTGATGCGTCG 57.908 33.333 0.58 0.00 0.00 5.12
2286 5280 7.796660 TGATACTAATAAAATTTGATGCGTCGC 59.203 33.333 11.10 11.10 0.00 5.19
2287 5281 5.874831 ACTAATAAAATTTGATGCGTCGCA 58.125 33.333 24.05 24.05 44.86 5.10
2288 5282 5.737290 ACTAATAAAATTTGATGCGTCGCAC 59.263 36.000 24.34 16.51 43.04 5.34
2289 5283 1.326576 AAAATTTGATGCGTCGCACG 58.673 45.000 24.34 0.00 43.04 5.34
2299 5293 4.874977 GTCGCACGCTAGGCTCCC 62.875 72.222 0.00 0.00 0.00 4.30
2301 5295 3.217017 CGCACGCTAGGCTCCCTA 61.217 66.667 0.00 0.00 34.61 3.53
2311 5305 2.041405 GCTCCCTAGCCAGGACCT 60.041 66.667 0.00 0.00 45.91 3.85
2312 5306 2.137528 GCTCCCTAGCCAGGACCTC 61.138 68.421 0.00 0.00 45.91 3.85
2313 5307 1.458588 CTCCCTAGCCAGGACCTCC 60.459 68.421 0.00 0.00 45.91 4.30
2314 5308 2.243774 CTCCCTAGCCAGGACCTCCA 62.244 65.000 0.00 0.00 45.91 3.86
2315 5309 1.306997 CCCTAGCCAGGACCTCCAA 60.307 63.158 0.00 0.00 45.91 3.53
2316 5310 0.695803 CCCTAGCCAGGACCTCCAAT 60.696 60.000 0.00 0.00 45.91 3.16
2317 5311 0.471617 CCTAGCCAGGACCTCCAATG 59.528 60.000 0.00 0.00 45.91 2.82
2318 5312 1.207791 CTAGCCAGGACCTCCAATGT 58.792 55.000 0.00 0.00 38.89 2.71
2319 5313 1.139853 CTAGCCAGGACCTCCAATGTC 59.860 57.143 0.00 0.00 38.89 3.06
2320 5314 1.450312 GCCAGGACCTCCAATGTCG 60.450 63.158 0.00 0.00 38.89 4.35
2321 5315 1.450312 CCAGGACCTCCAATGTCGC 60.450 63.158 0.00 0.00 38.89 5.19
2322 5316 1.296392 CAGGACCTCCAATGTCGCA 59.704 57.895 0.00 0.00 38.89 5.10
2323 5317 1.021390 CAGGACCTCCAATGTCGCAC 61.021 60.000 0.00 0.00 38.89 5.34
2324 5318 2.100631 GGACCTCCAATGTCGCACG 61.101 63.158 0.00 0.00 35.64 5.34
2325 5319 2.740714 GACCTCCAATGTCGCACGC 61.741 63.158 0.00 0.00 0.00 5.34
2326 5320 2.434884 CCTCCAATGTCGCACGCT 60.435 61.111 0.00 0.00 0.00 5.07
2327 5321 1.153647 CCTCCAATGTCGCACGCTA 60.154 57.895 0.00 0.00 0.00 4.26
2328 5322 1.148157 CCTCCAATGTCGCACGCTAG 61.148 60.000 0.00 0.00 0.00 3.42
2329 5323 1.148157 CTCCAATGTCGCACGCTAGG 61.148 60.000 0.00 0.00 0.00 3.02
2330 5324 2.703409 CAATGTCGCACGCTAGGC 59.297 61.111 0.00 0.00 0.00 3.93
2331 5325 1.811266 CAATGTCGCACGCTAGGCT 60.811 57.895 0.00 0.00 0.00 4.58
2332 5326 1.519455 AATGTCGCACGCTAGGCTC 60.519 57.895 0.00 0.00 0.00 4.70
2333 5327 2.225791 AATGTCGCACGCTAGGCTCA 62.226 55.000 0.00 0.00 0.00 4.26
2334 5328 2.881352 GTCGCACGCTAGGCTCAC 60.881 66.667 0.00 0.00 0.00 3.51
2335 5329 3.062466 TCGCACGCTAGGCTCACT 61.062 61.111 0.00 0.00 0.00 3.41
2336 5330 2.580867 CGCACGCTAGGCTCACTC 60.581 66.667 0.00 0.00 0.00 3.51
2337 5331 2.580867 GCACGCTAGGCTCACTCG 60.581 66.667 0.00 0.00 0.00 4.18
2338 5332 2.878429 CACGCTAGGCTCACTCGT 59.122 61.111 0.00 0.00 30.69 4.18
2339 5333 1.989966 GCACGCTAGGCTCACTCGTA 61.990 60.000 0.00 0.00 29.68 3.43
2340 5334 0.248134 CACGCTAGGCTCACTCGTAC 60.248 60.000 0.00 0.00 29.68 3.67
2341 5335 0.675837 ACGCTAGGCTCACTCGTACA 60.676 55.000 0.00 0.00 29.08 2.90
2342 5336 0.450583 CGCTAGGCTCACTCGTACAA 59.549 55.000 0.00 0.00 0.00 2.41
2343 5337 1.135489 CGCTAGGCTCACTCGTACAAA 60.135 52.381 0.00 0.00 0.00 2.83
2344 5338 2.670229 CGCTAGGCTCACTCGTACAAAA 60.670 50.000 0.00 0.00 0.00 2.44
2345 5339 3.522553 GCTAGGCTCACTCGTACAAAAT 58.477 45.455 0.00 0.00 0.00 1.82
2346 5340 3.552294 GCTAGGCTCACTCGTACAAAATC 59.448 47.826 0.00 0.00 0.00 2.17
2347 5341 3.678056 AGGCTCACTCGTACAAAATCA 57.322 42.857 0.00 0.00 0.00 2.57
2348 5342 4.002906 AGGCTCACTCGTACAAAATCAA 57.997 40.909 0.00 0.00 0.00 2.57
2349 5343 4.385825 AGGCTCACTCGTACAAAATCAAA 58.614 39.130 0.00 0.00 0.00 2.69
2350 5344 5.003804 AGGCTCACTCGTACAAAATCAAAT 58.996 37.500 0.00 0.00 0.00 2.32
2351 5345 5.473504 AGGCTCACTCGTACAAAATCAAATT 59.526 36.000 0.00 0.00 0.00 1.82
2352 5346 6.653320 AGGCTCACTCGTACAAAATCAAATTA 59.347 34.615 0.00 0.00 0.00 1.40
2353 5347 6.741358 GGCTCACTCGTACAAAATCAAATTAC 59.259 38.462 0.00 0.00 0.00 1.89
2354 5348 7.360946 GGCTCACTCGTACAAAATCAAATTACT 60.361 37.037 0.00 0.00 0.00 2.24
2355 5349 8.653338 GCTCACTCGTACAAAATCAAATTACTA 58.347 33.333 0.00 0.00 0.00 1.82
2357 5351 8.653338 TCACTCGTACAAAATCAAATTACTAGC 58.347 33.333 0.00 0.00 0.00 3.42
2358 5352 8.656849 CACTCGTACAAAATCAAATTACTAGCT 58.343 33.333 0.00 0.00 0.00 3.32
2359 5353 9.865321 ACTCGTACAAAATCAAATTACTAGCTA 57.135 29.630 0.00 0.00 0.00 3.32
2362 5356 9.864034 CGTACAAAATCAAATTACTAGCTATGG 57.136 33.333 0.00 0.00 0.00 2.74
2364 5358 7.716612 ACAAAATCAAATTACTAGCTATGGGC 58.283 34.615 0.00 0.00 42.19 5.36
2380 5374 7.709149 GCTATGGGCTATTGATCCTTTTATT 57.291 36.000 0.00 0.00 38.06 1.40
2381 5375 8.807948 GCTATGGGCTATTGATCCTTTTATTA 57.192 34.615 0.00 0.00 38.06 0.98
2382 5376 9.413734 GCTATGGGCTATTGATCCTTTTATTAT 57.586 33.333 0.00 0.00 38.06 1.28
2384 5378 8.599624 ATGGGCTATTGATCCTTTTATTATGG 57.400 34.615 0.00 0.00 0.00 2.74
2385 5379 6.953520 TGGGCTATTGATCCTTTTATTATGGG 59.046 38.462 0.00 0.00 0.00 4.00
2386 5380 6.127338 GGGCTATTGATCCTTTTATTATGGGC 60.127 42.308 0.00 0.00 0.00 5.36
2387 5381 6.127338 GGCTATTGATCCTTTTATTATGGGCC 60.127 42.308 0.00 0.00 0.00 5.80
2388 5382 5.982890 ATTGATCCTTTTATTATGGGCCG 57.017 39.130 0.00 0.00 0.00 6.13
2389 5383 4.447138 TGATCCTTTTATTATGGGCCGT 57.553 40.909 2.58 2.58 0.00 5.68
2390 5384 4.798882 TGATCCTTTTATTATGGGCCGTT 58.201 39.130 2.17 0.00 0.00 4.44
2391 5385 4.582656 TGATCCTTTTATTATGGGCCGTTG 59.417 41.667 2.17 0.00 0.00 4.10
2392 5386 3.292460 TCCTTTTATTATGGGCCGTTGG 58.708 45.455 2.17 0.00 0.00 3.77
2404 5398 2.734276 GCCGTTGGCCATCTTTTAAA 57.266 45.000 6.09 0.00 44.06 1.52
2405 5399 3.033368 GCCGTTGGCCATCTTTTAAAA 57.967 42.857 6.09 0.00 44.06 1.52
2406 5400 3.595173 GCCGTTGGCCATCTTTTAAAAT 58.405 40.909 6.09 0.00 44.06 1.82
2407 5401 4.000325 GCCGTTGGCCATCTTTTAAAATT 59.000 39.130 6.09 0.00 44.06 1.82
2408 5402 4.454161 GCCGTTGGCCATCTTTTAAAATTT 59.546 37.500 6.09 0.00 44.06 1.82
2409 5403 5.390461 GCCGTTGGCCATCTTTTAAAATTTC 60.390 40.000 6.09 0.00 44.06 2.17
2410 5404 5.121611 CCGTTGGCCATCTTTTAAAATTTCC 59.878 40.000 6.09 0.45 0.00 3.13
2411 5405 5.931724 CGTTGGCCATCTTTTAAAATTTCCT 59.068 36.000 6.09 0.00 0.00 3.36
2412 5406 6.128580 CGTTGGCCATCTTTTAAAATTTCCTG 60.129 38.462 6.09 0.00 0.00 3.86
2413 5407 5.803552 TGGCCATCTTTTAAAATTTCCTGG 58.196 37.500 0.00 5.75 0.00 4.45
2414 5408 4.635765 GGCCATCTTTTAAAATTTCCTGGC 59.364 41.667 20.13 20.13 44.54 4.85
2415 5409 5.244755 GCCATCTTTTAAAATTTCCTGGCA 58.755 37.500 21.77 0.00 44.63 4.92
2416 5410 5.704978 GCCATCTTTTAAAATTTCCTGGCAA 59.295 36.000 21.77 0.00 44.63 4.52
2417 5411 6.128200 GCCATCTTTTAAAATTTCCTGGCAAG 60.128 38.462 21.77 0.00 44.63 4.01
2418 5412 6.128200 CCATCTTTTAAAATTTCCTGGCAAGC 60.128 38.462 0.09 0.00 0.00 4.01
2419 5413 5.923204 TCTTTTAAAATTTCCTGGCAAGCA 58.077 33.333 0.09 0.00 0.00 3.91
2420 5414 5.990996 TCTTTTAAAATTTCCTGGCAAGCAG 59.009 36.000 0.09 0.00 0.00 4.24
2421 5415 2.845363 AAAATTTCCTGGCAAGCAGG 57.155 45.000 1.27 1.27 41.08 4.85
2422 5416 0.322648 AAATTTCCTGGCAAGCAGGC 59.677 50.000 2.79 0.00 39.60 4.85
2423 5417 0.543646 AATTTCCTGGCAAGCAGGCT 60.544 50.000 2.79 0.00 44.55 4.58
2424 5418 0.969409 ATTTCCTGGCAAGCAGGCTC 60.969 55.000 2.79 0.00 44.55 4.70
2425 5419 3.907260 TTCCTGGCAAGCAGGCTCG 62.907 63.158 2.79 0.00 44.55 5.03
2427 5421 4.711949 CTGGCAAGCAGGCTCGGT 62.712 66.667 0.00 0.00 44.55 4.69
2428 5422 3.315142 CTGGCAAGCAGGCTCGGTA 62.315 63.158 0.00 0.00 44.55 4.02
2429 5423 2.512515 GGCAAGCAGGCTCGGTAG 60.513 66.667 0.00 0.00 40.24 3.18
2430 5424 2.579201 GCAAGCAGGCTCGGTAGA 59.421 61.111 0.00 0.00 0.00 2.59
2431 5425 1.079127 GCAAGCAGGCTCGGTAGAA 60.079 57.895 0.00 0.00 0.00 2.10
2432 5426 0.673644 GCAAGCAGGCTCGGTAGAAA 60.674 55.000 0.00 0.00 0.00 2.52
2433 5427 1.808411 CAAGCAGGCTCGGTAGAAAA 58.192 50.000 0.00 0.00 0.00 2.29
2434 5428 2.151202 CAAGCAGGCTCGGTAGAAAAA 58.849 47.619 0.00 0.00 0.00 1.94
2435 5429 2.100605 AGCAGGCTCGGTAGAAAAAG 57.899 50.000 0.00 0.00 0.00 2.27
2436 5430 1.087501 GCAGGCTCGGTAGAAAAAGG 58.912 55.000 0.00 0.00 0.00 3.11
2437 5431 1.338769 GCAGGCTCGGTAGAAAAAGGA 60.339 52.381 0.00 0.00 0.00 3.36
2438 5432 2.622436 CAGGCTCGGTAGAAAAAGGAG 58.378 52.381 0.00 0.00 0.00 3.69
2439 5433 2.233922 CAGGCTCGGTAGAAAAAGGAGA 59.766 50.000 0.00 0.00 0.00 3.71
2440 5434 2.498078 AGGCTCGGTAGAAAAAGGAGAG 59.502 50.000 0.00 0.00 0.00 3.20
2441 5435 2.496470 GGCTCGGTAGAAAAAGGAGAGA 59.504 50.000 0.00 0.00 0.00 3.10
2442 5436 3.429684 GGCTCGGTAGAAAAAGGAGAGAG 60.430 52.174 0.00 0.00 0.00 3.20
2443 5437 3.444388 GCTCGGTAGAAAAAGGAGAGAGA 59.556 47.826 0.00 0.00 0.00 3.10
2444 5438 4.439563 GCTCGGTAGAAAAAGGAGAGAGAG 60.440 50.000 0.00 0.00 0.00 3.20
2445 5439 4.919793 TCGGTAGAAAAAGGAGAGAGAGA 58.080 43.478 0.00 0.00 0.00 3.10
2446 5440 4.944930 TCGGTAGAAAAAGGAGAGAGAGAG 59.055 45.833 0.00 0.00 0.00 3.20
2447 5441 4.944930 CGGTAGAAAAAGGAGAGAGAGAGA 59.055 45.833 0.00 0.00 0.00 3.10
2448 5442 5.065988 CGGTAGAAAAAGGAGAGAGAGAGAG 59.934 48.000 0.00 0.00 0.00 3.20
2449 5443 5.359860 GGTAGAAAAAGGAGAGAGAGAGAGG 59.640 48.000 0.00 0.00 0.00 3.69
2450 5444 4.352893 AGAAAAAGGAGAGAGAGAGAGGG 58.647 47.826 0.00 0.00 0.00 4.30
2451 5445 2.846665 AAAGGAGAGAGAGAGAGGGG 57.153 55.000 0.00 0.00 0.00 4.79
2452 5446 0.261696 AAGGAGAGAGAGAGAGGGGC 59.738 60.000 0.00 0.00 0.00 5.80
2453 5447 1.152546 GGAGAGAGAGAGAGGGGCC 60.153 68.421 0.00 0.00 0.00 5.80
2454 5448 1.655114 GGAGAGAGAGAGAGGGGCCT 61.655 65.000 0.84 0.00 0.00 5.19
2455 5449 0.261696 GAGAGAGAGAGAGGGGCCTT 59.738 60.000 0.84 0.00 0.00 4.35
2456 5450 0.715987 AGAGAGAGAGAGGGGCCTTT 59.284 55.000 0.84 0.00 0.00 3.11
2457 5451 1.080329 AGAGAGAGAGAGGGGCCTTTT 59.920 52.381 0.84 0.00 0.00 2.27
2458 5452 1.912731 GAGAGAGAGAGGGGCCTTTTT 59.087 52.381 0.84 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.694628 TCAAAAACATGCACCTGCTCTT 59.305 40.909 0.00 0.00 42.66 2.85
77 78 3.971702 GGCAAGCCACCTCCCAGT 61.972 66.667 6.14 0.00 35.81 4.00
85 86 3.506067 ACTTACAAAGTATGGCAAGCCAC 59.494 43.478 17.22 4.66 40.92 5.01
232 233 9.524106 TTAAGCATGAATCTATGAATTTTGCAG 57.476 29.630 0.00 0.00 33.74 4.41
273 276 9.039165 AGTGAAAGAATTTGGATTGTATGGAAT 57.961 29.630 0.00 0.00 39.27 3.01
289 746 9.232473 GGAGACAAATAAGGTAAGTGAAAGAAT 57.768 33.333 0.00 0.00 0.00 2.40
539 1016 4.621991 CATCTTACGGAAGACACCTATGG 58.378 47.826 13.53 0.00 44.50 2.74
612 1089 5.337169 GGAGAACTGCAGATAGAAAGTGTCT 60.337 44.000 23.35 6.37 40.71 3.41
616 1095 5.012561 AGTTGGAGAACTGCAGATAGAAAGT 59.987 40.000 23.35 7.43 41.12 2.66
701 1180 2.368221 AGTCTGATATCCTCAAGCAGCC 59.632 50.000 0.00 0.00 32.14 4.85
817 1299 0.531090 TTCCGTTCTGTCCACCAACG 60.531 55.000 0.00 0.00 42.02 4.10
828 1310 0.322546 GATTGCCCCTGTTCCGTTCT 60.323 55.000 0.00 0.00 0.00 3.01
996 1482 1.163420 TCTGCAAACGCAACATCGGT 61.163 50.000 0.00 0.00 39.39 4.69
1021 1507 2.612115 CCAGCCTCCAACTCCCCT 60.612 66.667 0.00 0.00 0.00 4.79
1047 1533 0.601046 CTTGAGCGTCACCTCTGCAA 60.601 55.000 0.00 0.00 33.02 4.08
1055 1541 1.419374 ACGAATGTCTTGAGCGTCAC 58.581 50.000 0.00 0.00 0.00 3.67
1305 1800 0.392327 TCGGCACATACACCACATGG 60.392 55.000 0.00 0.00 42.17 3.66
1419 2886 2.538449 GCCCGTCACATCACTAATTACG 59.462 50.000 0.00 0.00 0.00 3.18
1595 3156 2.607635 GAGAAGTCTGCAACGTTTGTGA 59.392 45.455 0.00 0.00 0.00 3.58
1729 4678 9.715121 AGAGTAACTAAATTACCGTGAATTCAA 57.285 29.630 10.35 0.00 43.82 2.69
1730 4679 9.715121 AAGAGTAACTAAATTACCGTGAATTCA 57.285 29.630 3.38 3.38 43.82 2.57
1733 4682 9.159364 GGAAAGAGTAACTAAATTACCGTGAAT 57.841 33.333 0.00 0.00 43.82 2.57
1734 4683 7.329226 CGGAAAGAGTAACTAAATTACCGTGAA 59.671 37.037 0.00 0.00 43.82 3.18
1756 4705 4.519350 AGCGACAAGTGATATAGATCGGAA 59.481 41.667 0.00 0.00 34.49 4.30
1867 4817 8.575589 CCTTAGGCCTTTTTGCAAAAATAAAAT 58.424 29.630 31.54 20.32 37.27 1.82
1872 4830 3.820467 GCCTTAGGCCTTTTTGCAAAAAT 59.180 39.130 31.54 21.37 44.06 1.82
1930 4892 1.003233 AACTTCGCAGCCCCTTCTC 60.003 57.895 0.00 0.00 0.00 2.87
1978 4972 0.107654 GTTTCCAGGGGATCTGTCCG 60.108 60.000 0.00 0.00 46.09 4.79
2024 5018 3.700538 CATGTGGATCTTTTTCCCTGGA 58.299 45.455 0.00 0.00 34.67 3.86
2027 5021 3.011032 AGAGCATGTGGATCTTTTTCCCT 59.989 43.478 0.00 0.00 39.85 4.20
2044 5038 0.108472 CTCATCGCCAGTGAAGAGCA 60.108 55.000 1.01 0.00 28.30 4.26
2047 5041 4.036852 CAGTATACTCATCGCCAGTGAAGA 59.963 45.833 1.26 0.00 0.00 2.87
2064 5058 3.129813 CACTACGTGCCACTTCCAGTATA 59.870 47.826 0.00 0.00 0.00 1.47
2135 5129 7.183460 AGGGAGAGACTACTAGTACAAATGTT 58.817 38.462 0.00 0.00 0.00 2.71
2136 5130 6.733509 AGGGAGAGACTACTAGTACAAATGT 58.266 40.000 0.00 0.00 0.00 2.71
2151 5145 5.927115 CCGTGCTTTATTATTAGGGAGAGAC 59.073 44.000 0.00 0.00 0.00 3.36
2152 5146 5.836898 TCCGTGCTTTATTATTAGGGAGAGA 59.163 40.000 0.00 0.00 0.00 3.10
2153 5147 6.097915 TCCGTGCTTTATTATTAGGGAGAG 57.902 41.667 0.00 0.00 0.00 3.20
2154 5148 6.681729 ATCCGTGCTTTATTATTAGGGAGA 57.318 37.500 0.00 0.00 0.00 3.71
2155 5149 6.934645 TCAATCCGTGCTTTATTATTAGGGAG 59.065 38.462 0.00 0.00 0.00 4.30
2156 5150 6.708949 GTCAATCCGTGCTTTATTATTAGGGA 59.291 38.462 0.00 0.00 0.00 4.20
2157 5151 6.710744 AGTCAATCCGTGCTTTATTATTAGGG 59.289 38.462 0.00 0.00 0.00 3.53
2158 5152 7.730364 AGTCAATCCGTGCTTTATTATTAGG 57.270 36.000 0.00 0.00 0.00 2.69
2159 5153 9.438291 CAAAGTCAATCCGTGCTTTATTATTAG 57.562 33.333 0.00 0.00 34.13 1.73
2160 5154 8.952278 ACAAAGTCAATCCGTGCTTTATTATTA 58.048 29.630 0.00 0.00 34.13 0.98
2161 5155 7.826690 ACAAAGTCAATCCGTGCTTTATTATT 58.173 30.769 0.00 0.00 34.13 1.40
2162 5156 7.391148 ACAAAGTCAATCCGTGCTTTATTAT 57.609 32.000 0.00 0.00 34.13 1.28
2163 5157 6.401688 CGACAAAGTCAATCCGTGCTTTATTA 60.402 38.462 0.00 0.00 34.13 0.98
2164 5158 5.616866 CGACAAAGTCAATCCGTGCTTTATT 60.617 40.000 0.00 0.00 34.13 1.40
2165 5159 4.142902 CGACAAAGTCAATCCGTGCTTTAT 60.143 41.667 0.00 0.00 34.13 1.40
2166 5160 3.185594 CGACAAAGTCAATCCGTGCTTTA 59.814 43.478 0.00 0.00 34.13 1.85
2167 5161 2.032030 CGACAAAGTCAATCCGTGCTTT 60.032 45.455 0.00 0.00 35.37 3.51
2168 5162 1.531149 CGACAAAGTCAATCCGTGCTT 59.469 47.619 0.00 0.00 32.09 3.91
2169 5163 1.148310 CGACAAAGTCAATCCGTGCT 58.852 50.000 0.00 0.00 32.09 4.40
2170 5164 0.165944 CCGACAAAGTCAATCCGTGC 59.834 55.000 0.00 0.00 32.09 5.34
2171 5165 0.796312 CCCGACAAAGTCAATCCGTG 59.204 55.000 0.00 0.00 32.09 4.94
2172 5166 0.395312 ACCCGACAAAGTCAATCCGT 59.605 50.000 0.00 0.00 32.09 4.69
2173 5167 1.463444 GAACCCGACAAAGTCAATCCG 59.537 52.381 0.00 0.00 32.09 4.18
2174 5168 2.225727 GTGAACCCGACAAAGTCAATCC 59.774 50.000 0.00 0.00 32.09 3.01
2175 5169 3.058914 CAGTGAACCCGACAAAGTCAATC 60.059 47.826 0.00 0.00 32.09 2.67
2176 5170 2.878406 CAGTGAACCCGACAAAGTCAAT 59.122 45.455 0.00 0.00 32.09 2.57
2177 5171 2.285083 CAGTGAACCCGACAAAGTCAA 58.715 47.619 0.00 0.00 32.09 3.18
2178 5172 1.208535 ACAGTGAACCCGACAAAGTCA 59.791 47.619 0.00 0.00 32.09 3.41
2179 5173 1.949465 ACAGTGAACCCGACAAAGTC 58.051 50.000 0.00 0.00 0.00 3.01
2180 5174 2.413310 AACAGTGAACCCGACAAAGT 57.587 45.000 0.00 0.00 0.00 2.66
2181 5175 3.199677 TGTAACAGTGAACCCGACAAAG 58.800 45.455 0.00 0.00 0.00 2.77
2182 5176 3.263489 TGTAACAGTGAACCCGACAAA 57.737 42.857 0.00 0.00 0.00 2.83
2183 5177 2.983907 TGTAACAGTGAACCCGACAA 57.016 45.000 0.00 0.00 0.00 3.18
2184 5178 2.983907 TTGTAACAGTGAACCCGACA 57.016 45.000 0.00 0.00 0.00 4.35
2185 5179 4.309099 TGTATTGTAACAGTGAACCCGAC 58.691 43.478 0.00 0.00 0.00 4.79
2186 5180 4.603989 TGTATTGTAACAGTGAACCCGA 57.396 40.909 0.00 0.00 0.00 5.14
2187 5181 5.873179 AATGTATTGTAACAGTGAACCCG 57.127 39.130 0.00 0.00 31.70 5.28
2188 5182 7.448748 AGAAATGTATTGTAACAGTGAACCC 57.551 36.000 0.00 0.00 31.70 4.11
2189 5183 8.784043 AGAAGAAATGTATTGTAACAGTGAACC 58.216 33.333 0.00 0.00 31.70 3.62
2190 5184 9.813080 GAGAAGAAATGTATTGTAACAGTGAAC 57.187 33.333 0.00 0.00 31.70 3.18
2191 5185 8.708742 CGAGAAGAAATGTATTGTAACAGTGAA 58.291 33.333 0.00 0.00 31.70 3.18
2192 5186 7.870954 ACGAGAAGAAATGTATTGTAACAGTGA 59.129 33.333 0.00 0.00 31.70 3.41
2193 5187 7.952101 CACGAGAAGAAATGTATTGTAACAGTG 59.048 37.037 0.00 0.00 31.70 3.66
2194 5188 7.870954 TCACGAGAAGAAATGTATTGTAACAGT 59.129 33.333 0.00 0.00 31.70 3.55
2195 5189 8.239681 TCACGAGAAGAAATGTATTGTAACAG 57.760 34.615 0.00 0.00 31.70 3.16
2196 5190 8.596271 TTCACGAGAAGAAATGTATTGTAACA 57.404 30.769 0.00 0.00 0.00 2.41
2202 5196 9.722056 GCATAAATTCACGAGAAGAAATGTATT 57.278 29.630 1.01 0.00 37.14 1.89
2203 5197 9.113838 AGCATAAATTCACGAGAAGAAATGTAT 57.886 29.630 1.01 0.00 37.14 2.29
2204 5198 8.492673 AGCATAAATTCACGAGAAGAAATGTA 57.507 30.769 1.01 0.00 37.14 2.29
2205 5199 7.383102 AGCATAAATTCACGAGAAGAAATGT 57.617 32.000 1.01 0.00 37.14 2.71
2206 5200 8.679288 AAAGCATAAATTCACGAGAAGAAATG 57.321 30.769 1.01 5.66 37.14 2.32
2240 5234 8.900781 AGTATCACCTCGCGTATATGTTATAAT 58.099 33.333 5.77 0.00 0.00 1.28
2241 5235 8.272545 AGTATCACCTCGCGTATATGTTATAA 57.727 34.615 5.77 0.00 0.00 0.98
2242 5236 7.854557 AGTATCACCTCGCGTATATGTTATA 57.145 36.000 5.77 0.00 0.00 0.98
2243 5237 6.754702 AGTATCACCTCGCGTATATGTTAT 57.245 37.500 5.77 0.00 0.00 1.89
2244 5238 7.671495 TTAGTATCACCTCGCGTATATGTTA 57.329 36.000 5.77 0.00 0.00 2.41
2245 5239 6.564709 TTAGTATCACCTCGCGTATATGTT 57.435 37.500 5.77 0.00 0.00 2.71
2246 5240 6.754702 ATTAGTATCACCTCGCGTATATGT 57.245 37.500 5.77 0.00 0.00 2.29
2247 5241 9.563898 TTTTATTAGTATCACCTCGCGTATATG 57.436 33.333 5.77 0.70 0.00 1.78
2250 5244 9.485206 AAATTTTATTAGTATCACCTCGCGTAT 57.515 29.630 5.77 0.00 0.00 3.06
2251 5245 8.757789 CAAATTTTATTAGTATCACCTCGCGTA 58.242 33.333 5.77 0.00 0.00 4.42
2252 5246 7.493320 TCAAATTTTATTAGTATCACCTCGCGT 59.507 33.333 5.77 0.00 0.00 6.01
2253 5247 7.847487 TCAAATTTTATTAGTATCACCTCGCG 58.153 34.615 0.00 0.00 0.00 5.87
2254 5248 9.599322 CATCAAATTTTATTAGTATCACCTCGC 57.401 33.333 0.00 0.00 0.00 5.03
2255 5249 9.599322 GCATCAAATTTTATTAGTATCACCTCG 57.401 33.333 0.00 0.00 0.00 4.63
2256 5250 9.599322 CGCATCAAATTTTATTAGTATCACCTC 57.401 33.333 0.00 0.00 0.00 3.85
2257 5251 9.120538 ACGCATCAAATTTTATTAGTATCACCT 57.879 29.630 0.00 0.00 0.00 4.00
2258 5252 9.382244 GACGCATCAAATTTTATTAGTATCACC 57.618 33.333 0.00 0.00 0.00 4.02
2259 5253 9.092322 CGACGCATCAAATTTTATTAGTATCAC 57.908 33.333 0.00 0.00 0.00 3.06
2260 5254 7.796660 GCGACGCATCAAATTTTATTAGTATCA 59.203 33.333 16.42 0.00 0.00 2.15
2261 5255 7.796660 TGCGACGCATCAAATTTTATTAGTATC 59.203 33.333 20.50 0.00 31.71 2.24
2262 5256 7.586300 GTGCGACGCATCAAATTTTATTAGTAT 59.414 33.333 27.23 0.00 41.91 2.12
2263 5257 6.902948 GTGCGACGCATCAAATTTTATTAGTA 59.097 34.615 27.23 0.00 41.91 1.82
2264 5258 5.737290 GTGCGACGCATCAAATTTTATTAGT 59.263 36.000 27.23 0.00 41.91 2.24
2265 5259 5.109150 CGTGCGACGCATCAAATTTTATTAG 60.109 40.000 27.23 0.00 41.91 1.73
2266 5260 4.726229 CGTGCGACGCATCAAATTTTATTA 59.274 37.500 27.23 0.00 41.91 0.98
2267 5261 3.541916 CGTGCGACGCATCAAATTTTATT 59.458 39.130 27.23 0.00 41.91 1.40
2268 5262 3.097910 CGTGCGACGCATCAAATTTTAT 58.902 40.909 27.23 0.00 41.91 1.40
2269 5263 2.500888 CGTGCGACGCATCAAATTTTA 58.499 42.857 27.23 0.00 41.91 1.52
2270 5264 1.326576 CGTGCGACGCATCAAATTTT 58.673 45.000 27.23 0.00 41.91 1.82
2271 5265 3.000164 CGTGCGACGCATCAAATTT 58.000 47.368 27.23 0.00 41.91 1.82
2272 5266 4.743558 CGTGCGACGCATCAAATT 57.256 50.000 27.23 0.00 41.91 1.82
2282 5276 4.874977 GGGAGCCTAGCGTGCGAC 62.875 72.222 0.00 0.00 0.00 5.19
2283 5277 3.709348 TAGGGAGCCTAGCGTGCGA 62.709 63.158 0.00 0.00 34.61 5.10
2284 5278 3.200887 CTAGGGAGCCTAGCGTGCG 62.201 68.421 0.00 0.00 45.64 5.34
2285 5279 2.731374 CTAGGGAGCCTAGCGTGC 59.269 66.667 0.00 0.00 45.64 5.34
2295 5289 1.458588 GGAGGTCCTGGCTAGGGAG 60.459 68.421 17.16 0.00 44.70 4.30
2296 5290 1.821966 TTGGAGGTCCTGGCTAGGGA 61.822 60.000 17.16 2.41 44.70 4.20
2297 5291 0.695803 ATTGGAGGTCCTGGCTAGGG 60.696 60.000 17.16 0.00 44.70 3.53
2298 5292 0.471617 CATTGGAGGTCCTGGCTAGG 59.528 60.000 10.47 10.47 46.06 3.02
2299 5293 1.139853 GACATTGGAGGTCCTGGCTAG 59.860 57.143 0.00 0.00 36.82 3.42
2300 5294 1.204146 GACATTGGAGGTCCTGGCTA 58.796 55.000 0.00 0.00 36.82 3.93
2301 5295 1.903877 CGACATTGGAGGTCCTGGCT 61.904 60.000 0.00 0.00 36.82 4.75
2302 5296 1.450312 CGACATTGGAGGTCCTGGC 60.450 63.158 0.00 0.00 36.82 4.85
2303 5297 1.450312 GCGACATTGGAGGTCCTGG 60.450 63.158 0.00 0.00 36.82 4.45
2304 5298 1.021390 GTGCGACATTGGAGGTCCTG 61.021 60.000 0.00 0.00 36.82 3.86
2305 5299 1.296715 GTGCGACATTGGAGGTCCT 59.703 57.895 0.00 0.00 36.82 3.85
2306 5300 2.100631 CGTGCGACATTGGAGGTCC 61.101 63.158 0.00 0.00 31.55 4.46
2307 5301 2.740714 GCGTGCGACATTGGAGGTC 61.741 63.158 0.00 0.00 0.00 3.85
2308 5302 1.884075 TAGCGTGCGACATTGGAGGT 61.884 55.000 0.00 0.00 0.00 3.85
2309 5303 1.148157 CTAGCGTGCGACATTGGAGG 61.148 60.000 0.00 0.00 0.00 4.30
2310 5304 1.148157 CCTAGCGTGCGACATTGGAG 61.148 60.000 0.00 0.00 0.00 3.86
2311 5305 1.153647 CCTAGCGTGCGACATTGGA 60.154 57.895 0.00 0.00 0.00 3.53
2312 5306 2.813179 GCCTAGCGTGCGACATTGG 61.813 63.158 0.00 0.00 0.00 3.16
2313 5307 1.756375 GAGCCTAGCGTGCGACATTG 61.756 60.000 0.00 0.00 0.00 2.82
2314 5308 1.519455 GAGCCTAGCGTGCGACATT 60.519 57.895 0.00 0.00 0.00 2.71
2315 5309 2.105128 GAGCCTAGCGTGCGACAT 59.895 61.111 0.00 0.00 0.00 3.06
2316 5310 3.370231 TGAGCCTAGCGTGCGACA 61.370 61.111 0.00 0.00 0.00 4.35
2317 5311 2.881352 GTGAGCCTAGCGTGCGAC 60.881 66.667 0.00 0.00 0.00 5.19
2318 5312 3.052620 GAGTGAGCCTAGCGTGCGA 62.053 63.158 0.00 0.00 0.00 5.10
2319 5313 2.580867 GAGTGAGCCTAGCGTGCG 60.581 66.667 0.00 0.00 0.00 5.34
2320 5314 1.989966 TACGAGTGAGCCTAGCGTGC 61.990 60.000 0.00 0.00 36.51 5.34
2321 5315 0.248134 GTACGAGTGAGCCTAGCGTG 60.248 60.000 0.00 0.00 36.51 5.34
2322 5316 0.675837 TGTACGAGTGAGCCTAGCGT 60.676 55.000 0.00 0.00 38.81 5.07
2323 5317 0.450583 TTGTACGAGTGAGCCTAGCG 59.549 55.000 0.00 0.00 0.00 4.26
2324 5318 2.649331 TTTGTACGAGTGAGCCTAGC 57.351 50.000 0.00 0.00 0.00 3.42
2325 5319 4.744570 TGATTTTGTACGAGTGAGCCTAG 58.255 43.478 0.00 0.00 0.00 3.02
2326 5320 4.794278 TGATTTTGTACGAGTGAGCCTA 57.206 40.909 0.00 0.00 0.00 3.93
2327 5321 3.678056 TGATTTTGTACGAGTGAGCCT 57.322 42.857 0.00 0.00 0.00 4.58
2328 5322 4.742438 TTTGATTTTGTACGAGTGAGCC 57.258 40.909 0.00 0.00 0.00 4.70
2329 5323 7.519002 AGTAATTTGATTTTGTACGAGTGAGC 58.481 34.615 0.00 0.00 0.00 4.26
2331 5325 8.653338 GCTAGTAATTTGATTTTGTACGAGTGA 58.347 33.333 0.00 0.00 0.00 3.41
2332 5326 8.656849 AGCTAGTAATTTGATTTTGTACGAGTG 58.343 33.333 0.00 0.00 0.00 3.51
2333 5327 8.773404 AGCTAGTAATTTGATTTTGTACGAGT 57.227 30.769 0.00 0.00 0.00 4.18
2336 5330 9.864034 CCATAGCTAGTAATTTGATTTTGTACG 57.136 33.333 0.00 0.00 0.00 3.67
2338 5332 8.846211 GCCCATAGCTAGTAATTTGATTTTGTA 58.154 33.333 0.00 0.00 38.99 2.41
2339 5333 7.716612 GCCCATAGCTAGTAATTTGATTTTGT 58.283 34.615 0.00 0.00 38.99 2.83
2356 5350 7.709149 AATAAAAGGATCAATAGCCCATAGC 57.291 36.000 0.00 0.00 44.25 2.97
2358 5352 9.699410 CCATAATAAAAGGATCAATAGCCCATA 57.301 33.333 0.00 0.00 0.00 2.74
2359 5353 7.620888 CCCATAATAAAAGGATCAATAGCCCAT 59.379 37.037 0.00 0.00 0.00 4.00
2360 5354 6.953520 CCCATAATAAAAGGATCAATAGCCCA 59.046 38.462 0.00 0.00 0.00 5.36
2361 5355 6.127338 GCCCATAATAAAAGGATCAATAGCCC 60.127 42.308 0.00 0.00 0.00 5.19
2362 5356 6.127338 GGCCCATAATAAAAGGATCAATAGCC 60.127 42.308 0.00 0.00 0.00 3.93
2363 5357 6.404734 CGGCCCATAATAAAAGGATCAATAGC 60.405 42.308 0.00 0.00 0.00 2.97
2364 5358 6.659242 ACGGCCCATAATAAAAGGATCAATAG 59.341 38.462 0.00 0.00 0.00 1.73
2365 5359 6.548321 ACGGCCCATAATAAAAGGATCAATA 58.452 36.000 0.00 0.00 0.00 1.90
2366 5360 5.393866 ACGGCCCATAATAAAAGGATCAAT 58.606 37.500 0.00 0.00 0.00 2.57
2367 5361 4.798882 ACGGCCCATAATAAAAGGATCAA 58.201 39.130 0.00 0.00 0.00 2.57
2368 5362 4.447138 ACGGCCCATAATAAAAGGATCA 57.553 40.909 0.00 0.00 0.00 2.92
2369 5363 4.022329 CCAACGGCCCATAATAAAAGGATC 60.022 45.833 0.00 0.00 0.00 3.36
2370 5364 3.895041 CCAACGGCCCATAATAAAAGGAT 59.105 43.478 0.00 0.00 0.00 3.24
2371 5365 3.292460 CCAACGGCCCATAATAAAAGGA 58.708 45.455 0.00 0.00 0.00 3.36
2372 5366 2.223947 GCCAACGGCCCATAATAAAAGG 60.224 50.000 0.00 0.00 44.06 3.11
2373 5367 3.092334 GCCAACGGCCCATAATAAAAG 57.908 47.619 0.00 0.00 44.06 2.27
2386 5380 5.121611 GGAAATTTTAAAAGATGGCCAACGG 59.878 40.000 10.96 0.00 0.00 4.44
2387 5381 5.931724 AGGAAATTTTAAAAGATGGCCAACG 59.068 36.000 10.96 0.00 0.00 4.10
2388 5382 6.149308 CCAGGAAATTTTAAAAGATGGCCAAC 59.851 38.462 10.96 7.42 0.00 3.77
2389 5383 6.237154 CCAGGAAATTTTAAAAGATGGCCAA 58.763 36.000 10.96 0.00 0.00 4.52
2390 5384 5.802821 GCCAGGAAATTTTAAAAGATGGCCA 60.803 40.000 21.87 8.56 43.81 5.36
2391 5385 4.635765 GCCAGGAAATTTTAAAAGATGGCC 59.364 41.667 21.87 0.00 43.81 5.36
2392 5386 5.801350 GCCAGGAAATTTTAAAAGATGGC 57.199 39.130 19.78 19.78 43.33 4.40
2393 5387 6.128200 GCTTGCCAGGAAATTTTAAAAGATGG 60.128 38.462 6.79 10.06 0.00 3.51
2394 5388 6.427547 TGCTTGCCAGGAAATTTTAAAAGATG 59.572 34.615 6.79 1.24 0.00 2.90
2395 5389 6.532826 TGCTTGCCAGGAAATTTTAAAAGAT 58.467 32.000 6.79 0.00 0.00 2.40
2396 5390 5.923204 TGCTTGCCAGGAAATTTTAAAAGA 58.077 33.333 6.79 0.00 0.00 2.52
2397 5391 6.232139 CTGCTTGCCAGGAAATTTTAAAAG 57.768 37.500 6.79 0.00 37.93 2.27
2410 5404 3.315142 TACCGAGCCTGCTTGCCAG 62.315 63.158 0.56 0.00 41.41 4.85
2411 5405 3.315142 CTACCGAGCCTGCTTGCCA 62.315 63.158 0.56 0.00 0.00 4.92
2412 5406 2.512515 CTACCGAGCCTGCTTGCC 60.513 66.667 0.56 0.00 0.00 4.52
2413 5407 0.673644 TTTCTACCGAGCCTGCTTGC 60.674 55.000 0.56 0.00 0.00 4.01
2414 5408 1.808411 TTTTCTACCGAGCCTGCTTG 58.192 50.000 0.00 0.00 0.00 4.01
2415 5409 2.427506 CTTTTTCTACCGAGCCTGCTT 58.572 47.619 0.00 0.00 0.00 3.91
2416 5410 1.339151 CCTTTTTCTACCGAGCCTGCT 60.339 52.381 0.00 0.00 0.00 4.24
2417 5411 1.087501 CCTTTTTCTACCGAGCCTGC 58.912 55.000 0.00 0.00 0.00 4.85
2418 5412 2.233922 TCTCCTTTTTCTACCGAGCCTG 59.766 50.000 0.00 0.00 0.00 4.85
2419 5413 2.498078 CTCTCCTTTTTCTACCGAGCCT 59.502 50.000 0.00 0.00 0.00 4.58
2420 5414 2.496470 TCTCTCCTTTTTCTACCGAGCC 59.504 50.000 0.00 0.00 0.00 4.70
2421 5415 3.444388 TCTCTCTCCTTTTTCTACCGAGC 59.556 47.826 0.00 0.00 0.00 5.03
2422 5416 4.944930 TCTCTCTCTCCTTTTTCTACCGAG 59.055 45.833 0.00 0.00 0.00 4.63
2423 5417 4.919793 TCTCTCTCTCCTTTTTCTACCGA 58.080 43.478 0.00 0.00 0.00 4.69
2424 5418 4.944930 TCTCTCTCTCTCCTTTTTCTACCG 59.055 45.833 0.00 0.00 0.00 4.02
2425 5419 5.359860 CCTCTCTCTCTCTCCTTTTTCTACC 59.640 48.000 0.00 0.00 0.00 3.18
2426 5420 5.359860 CCCTCTCTCTCTCTCCTTTTTCTAC 59.640 48.000 0.00 0.00 0.00 2.59
2427 5421 5.515106 CCCTCTCTCTCTCTCCTTTTTCTA 58.485 45.833 0.00 0.00 0.00 2.10
2428 5422 4.352893 CCCTCTCTCTCTCTCCTTTTTCT 58.647 47.826 0.00 0.00 0.00 2.52
2429 5423 3.450817 CCCCTCTCTCTCTCTCCTTTTTC 59.549 52.174 0.00 0.00 0.00 2.29
2430 5424 3.449918 CCCCTCTCTCTCTCTCCTTTTT 58.550 50.000 0.00 0.00 0.00 1.94
2431 5425 2.892301 GCCCCTCTCTCTCTCTCCTTTT 60.892 54.545 0.00 0.00 0.00 2.27
2432 5426 1.342975 GCCCCTCTCTCTCTCTCCTTT 60.343 57.143 0.00 0.00 0.00 3.11
2433 5427 0.261696 GCCCCTCTCTCTCTCTCCTT 59.738 60.000 0.00 0.00 0.00 3.36
2434 5428 1.655114 GGCCCCTCTCTCTCTCTCCT 61.655 65.000 0.00 0.00 0.00 3.69
2435 5429 1.152546 GGCCCCTCTCTCTCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
2436 5430 0.261696 AAGGCCCCTCTCTCTCTCTC 59.738 60.000 0.00 0.00 0.00 3.20
2437 5431 0.715987 AAAGGCCCCTCTCTCTCTCT 59.284 55.000 0.00 0.00 0.00 3.10
2438 5432 1.578897 AAAAGGCCCCTCTCTCTCTC 58.421 55.000 0.00 0.00 0.00 3.20
2439 5433 2.052249 AAAAAGGCCCCTCTCTCTCT 57.948 50.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.