Multiple sequence alignment - TraesCS7D01G177700

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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 TraesCS7D01G177700 chr7D 100.000 3150 0 0 1 3150 130925705 130922556 0.000000e+00 5818.0
1 TraesCS7D01G177700 chr7D 88.142 818 79 13 2282 3082 184817893 184818709 0.000000e+00 957.0
2 TraesCS7D01G177700 chr7D 83.875 769 103 15 2330 3088 465572345 465571588 0.000000e+00 713.0
3 TraesCS7D01G177700 chr7D 92.308 91 6 1 1701 1791 83663361 83663272 9.170000e-26 128.0
4 TraesCS7D01G177700 chr7D 87.273 110 12 2 1701 1810 83754975 83754868 1.190000e-24 124.0
5 TraesCS7D01G177700 chr7D 98.529 68 1 0 3083 3150 238968420 238968353 1.530000e-23 121.0
6 TraesCS7D01G177700 chr7B 89.871 2172 122 34 33 2143 92016330 92014196 0.000000e+00 2702.0
7 TraesCS7D01G177700 chr7B 92.771 83 6 0 1709 1791 33414628 33414546 1.530000e-23 121.0
8 TraesCS7D01G177700 chr7B 90.000 90 8 1 1701 1790 33528597 33528509 7.140000e-22 115.0
9 TraesCS7D01G177700 chr7A 87.678 2102 140 46 11 2025 129705970 129703901 0.000000e+00 2337.0
10 TraesCS7D01G177700 chr7A 86.455 694 89 5 2399 3088 244602048 244601356 0.000000e+00 756.0
11 TraesCS7D01G177700 chr7A 88.136 118 10 1 2158 2275 725929435 725929322 1.520000e-28 137.0
12 TraesCS7D01G177700 chr7A 91.209 91 7 1 1701 1791 85347332 85347243 4.270000e-24 122.0
13 TraesCS7D01G177700 chr7A 83.206 131 15 4 1701 1831 85412419 85412296 2.570000e-21 113.0
14 TraesCS7D01G177700 chr6B 87.454 821 70 19 2280 3082 408492282 408493087 0.000000e+00 915.0
15 TraesCS7D01G177700 chr6B 84.249 546 73 10 2280 2815 114268730 114269272 1.290000e-143 520.0
16 TraesCS7D01G177700 chr6B 88.983 118 12 1 2158 2274 278154800 278154917 9.110000e-31 145.0
17 TraesCS7D01G177700 chr5D 85.086 818 104 12 2282 3082 372097337 372098153 0.000000e+00 819.0
18 TraesCS7D01G177700 chr5A 86.262 757 99 5 2330 3082 475351776 475351021 0.000000e+00 817.0
19 TraesCS7D01G177700 chr5A 98.529 68 1 0 3083 3150 674217945 674217878 1.530000e-23 121.0
20 TraesCS7D01G177700 chr4B 86.074 754 86 14 2337 3082 397038274 397039016 0.000000e+00 793.0
21 TraesCS7D01G177700 chr4B 98.529 68 1 0 3083 3150 382779292 382779225 1.530000e-23 121.0
22 TraesCS7D01G177700 chr4B 98.529 68 1 0 3083 3150 472743106 472743173 1.530000e-23 121.0
23 TraesCS7D01G177700 chr2D 86.351 718 83 10 2378 3088 204990509 204989800 0.000000e+00 769.0
24 TraesCS7D01G177700 chr1D 88.283 623 70 3 2282 2902 460171681 460172302 0.000000e+00 743.0
25 TraesCS7D01G177700 chr1D 93.220 118 7 1 2158 2274 298576993 298577110 4.180000e-39 172.0
26 TraesCS7D01G177700 chr1D 90.678 118 6 3 2158 2274 12331973 12331860 5.440000e-33 152.0
27 TraesCS7D01G177700 chr1D 98.529 68 1 0 3083 3150 62961566 62961633 1.530000e-23 121.0
28 TraesCS7D01G177700 chr1B 85.211 710 85 15 2278 2973 61475382 61474679 0.000000e+00 712.0
29 TraesCS7D01G177700 chr1B 98.529 68 1 0 3083 3150 592644121 592644054 1.530000e-23 121.0
30 TraesCS7D01G177700 chr2A 82.073 820 125 16 2282 3082 779639032 779639848 0.000000e+00 680.0
31 TraesCS7D01G177700 chr3A 92.308 117 9 0 2158 2274 37802202 37802086 1.940000e-37 167.0
32 TraesCS7D01G177700 chr3A 87.302 126 8 2 2157 2274 453659614 453659739 1.520000e-28 137.0
33 TraesCS7D01G177700 chr1A 89.167 120 12 1 2156 2274 50963525 50963644 7.040000e-32 148.0
34 TraesCS7D01G177700 chr4A 87.395 119 13 1 2158 2274 440873092 440872974 5.480000e-28 135.0
35 TraesCS7D01G177700 chr5B 87.097 124 9 4 2156 2274 265435347 265435468 1.970000e-27 134.0
36 TraesCS7D01G177700 chr5B 98.529 68 1 0 3083 3150 510832114 510832181 1.530000e-23 121.0
37 TraesCS7D01G177700 chr5B 82.653 98 10 6 2108 2201 145670924 145670830 2.600000e-11 80.5
38 TraesCS7D01G177700 chr3B 100.000 68 0 0 3083 3150 628718931 628718864 3.300000e-25 126.0
39 TraesCS7D01G177700 chr4D 98.529 68 1 0 3083 3150 488176485 488176418 1.530000e-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 TraesCS7D01G177700 chr7D 130922556 130925705 3149 True 5818 5818 100.000 1 3150 1 chr7D.!!$R3 3149
1 TraesCS7D01G177700 chr7D 184817893 184818709 816 False 957 957 88.142 2282 3082 1 chr7D.!!$F1 800
2 TraesCS7D01G177700 chr7D 465571588 465572345 757 True 713 713 83.875 2330 3088 1 chr7D.!!$R5 758
3 TraesCS7D01G177700 chr7B 92014196 92016330 2134 True 2702 2702 89.871 33 2143 1 chr7B.!!$R3 2110
4 TraesCS7D01G177700 chr7A 129703901 129705970 2069 True 2337 2337 87.678 11 2025 1 chr7A.!!$R3 2014
5 TraesCS7D01G177700 chr7A 244601356 244602048 692 True 756 756 86.455 2399 3088 1 chr7A.!!$R4 689
6 TraesCS7D01G177700 chr6B 408492282 408493087 805 False 915 915 87.454 2280 3082 1 chr6B.!!$F3 802
7 TraesCS7D01G177700 chr6B 114268730 114269272 542 False 520 520 84.249 2280 2815 1 chr6B.!!$F1 535
8 TraesCS7D01G177700 chr5D 372097337 372098153 816 False 819 819 85.086 2282 3082 1 chr5D.!!$F1 800
9 TraesCS7D01G177700 chr5A 475351021 475351776 755 True 817 817 86.262 2330 3082 1 chr5A.!!$R1 752
10 TraesCS7D01G177700 chr4B 397038274 397039016 742 False 793 793 86.074 2337 3082 1 chr4B.!!$F1 745
11 TraesCS7D01G177700 chr2D 204989800 204990509 709 True 769 769 86.351 2378 3088 1 chr2D.!!$R1 710
12 TraesCS7D01G177700 chr1D 460171681 460172302 621 False 743 743 88.283 2282 2902 1 chr1D.!!$F3 620
13 TraesCS7D01G177700 chr1B 61474679 61475382 703 True 712 712 85.211 2278 2973 1 chr1B.!!$R1 695
14 TraesCS7D01G177700 chr2A 779639032 779639848 816 False 680 680 82.073 2282 3082 1 chr2A.!!$F1 800

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
505 514 0.699399 AGGGAACAGAGTCGGAGAGA 59.301 55.0 0.0 0.0 36.95 3.10 F
1746 1833 0.250901 AGCAGTTCATCCGGCAGTTT 60.251 50.0 0.0 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2102 0.103755 TGAGAGATGTGCGATCTGCC 59.896 55.0 2.87 0.0 45.6 4.85 R
2665 2807 0.103572 GTAGGAAATACGAGGCGGCA 59.896 55.0 13.08 0.0 0.0 5.69 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
65 66 5.872070 GCTAGAGTTGCTCTAATTTGTCTGT 59.128 40.000 7.22 0.00 41.74 3.41
67 68 4.926238 AGAGTTGCTCTAATTTGTCTGTCG 59.074 41.667 0.00 0.00 39.28 4.35
68 69 4.883083 AGTTGCTCTAATTTGTCTGTCGA 58.117 39.130 0.00 0.00 0.00 4.20
71 72 5.072040 TGCTCTAATTTGTCTGTCGATCA 57.928 39.130 0.00 0.00 0.00 2.92
155 156 2.601763 CCACTAGATTTGTAACGCGGAC 59.398 50.000 12.47 8.97 0.00 4.79
342 345 3.052082 CCTTGCACGCCAGTCCAG 61.052 66.667 0.00 0.00 0.00 3.86
499 508 1.374758 GGCACAGGGAACAGAGTCG 60.375 63.158 0.00 0.00 0.00 4.18
505 514 0.699399 AGGGAACAGAGTCGGAGAGA 59.301 55.000 0.00 0.00 36.95 3.10
506 515 1.099689 GGGAACAGAGTCGGAGAGAG 58.900 60.000 0.00 0.00 36.95 3.20
689 718 3.604667 CTGCCCAAGTTGCCGCAA 61.605 61.111 14.49 0.38 0.00 4.85
706 735 1.455402 AAGCCACACACCACATGCA 60.455 52.632 0.00 0.00 0.00 3.96
859 896 3.366629 GAGCTGTCACGGTCCAGA 58.633 61.111 0.00 0.00 0.00 3.86
860 897 1.080434 GAGCTGTCACGGTCCAGAC 60.080 63.158 0.00 4.82 35.37 3.51
868 905 1.979693 ACGGTCCAGACTCCAGAGC 60.980 63.158 0.00 0.00 0.00 4.09
910 948 1.584380 CTGAGCTGAGCAAAGGCACC 61.584 60.000 7.39 0.00 44.61 5.01
923 961 1.609208 AGGCACCGCATTATTCATCC 58.391 50.000 0.00 0.00 0.00 3.51
924 962 1.133823 AGGCACCGCATTATTCATCCA 60.134 47.619 0.00 0.00 0.00 3.41
927 965 2.095059 GCACCGCATTATTCATCCATCC 60.095 50.000 0.00 0.00 0.00 3.51
928 966 2.160219 CACCGCATTATTCATCCATCCG 59.840 50.000 0.00 0.00 0.00 4.18
929 967 2.224523 ACCGCATTATTCATCCATCCGT 60.225 45.455 0.00 0.00 0.00 4.69
974 1036 1.781786 CAAGAAGATCGGGAGGAGGA 58.218 55.000 0.00 0.00 0.00 3.71
988 1050 2.962421 GAGGAGGATCGGAGTTTGATCT 59.038 50.000 0.00 0.00 41.56 2.75
1158 1221 4.430423 CGCAAGCTCGTTCGCACC 62.430 66.667 0.00 0.00 0.00 5.01
1181 1244 2.338620 CACCGTCGTGCTGGAGAA 59.661 61.111 0.00 0.00 32.04 2.87
1280 1343 2.280797 GCTCCACCACGTGCAAGA 60.281 61.111 10.91 4.74 31.34 3.02
1285 1348 2.111043 ACCACGTGCAAGACCAGG 59.889 61.111 10.91 5.25 0.00 4.45
1287 1350 1.669115 CCACGTGCAAGACCAGGAG 60.669 63.158 10.91 0.00 0.00 3.69
1294 1363 2.165845 GTGCAAGACCAGGAGTATACGT 59.834 50.000 0.00 0.00 0.00 3.57
1296 1365 3.259876 TGCAAGACCAGGAGTATACGTTT 59.740 43.478 0.00 0.00 0.00 3.60
1298 1367 4.103357 CAAGACCAGGAGTATACGTTTCG 58.897 47.826 0.00 0.00 0.00 3.46
1305 1374 3.312973 AGGAGTATACGTTTCGAGAGCAG 59.687 47.826 0.00 0.00 0.00 4.24
1308 1377 2.853731 ATACGTTTCGAGAGCAGGAG 57.146 50.000 0.00 0.00 0.00 3.69
1310 1379 1.179814 ACGTTTCGAGAGCAGGAGGT 61.180 55.000 0.00 0.00 0.00 3.85
1327 1396 1.681327 GTACGGGAGGTGAGCAGGA 60.681 63.158 0.00 0.00 0.00 3.86
1329 1398 0.554305 TACGGGAGGTGAGCAGGATA 59.446 55.000 0.00 0.00 0.00 2.59
1333 1402 1.412361 GGGAGGTGAGCAGGATAGAGT 60.412 57.143 0.00 0.00 0.00 3.24
1451 1520 0.326264 GTGAACAGGATGGTGGAGCT 59.674 55.000 0.00 0.00 33.00 4.09
1456 1525 1.000993 AGGATGGTGGAGCTCGAGT 59.999 57.895 15.13 0.23 0.00 4.18
1574 1643 1.227002 CTAAGGGCGAGGTCGAAGC 60.227 63.158 2.94 0.00 43.02 3.86
1746 1833 0.250901 AGCAGTTCATCCGGCAGTTT 60.251 50.000 0.00 0.00 0.00 2.66
1878 1970 4.035792 CGTTTGATCGTGTAGAGAGAGGAT 59.964 45.833 0.00 0.00 0.00 3.24
1953 2046 2.805671 CGACAGCACACAGTTTTGGATA 59.194 45.455 0.00 0.00 0.00 2.59
1954 2047 3.436704 CGACAGCACACAGTTTTGGATAT 59.563 43.478 0.00 0.00 0.00 1.63
1955 2048 4.669965 CGACAGCACACAGTTTTGGATATG 60.670 45.833 0.00 0.00 0.00 1.78
1958 2051 5.068987 ACAGCACACAGTTTTGGATATGTTT 59.931 36.000 0.00 0.00 0.00 2.83
1998 2100 2.919666 ACTGCCAAAACATCGCATAC 57.080 45.000 0.00 0.00 0.00 2.39
2000 2102 2.162208 ACTGCCAAAACATCGCATACTG 59.838 45.455 0.00 0.00 0.00 2.74
2007 2109 2.160822 ACATCGCATACTGGCAGATC 57.839 50.000 23.66 5.79 0.00 2.75
2026 2128 1.690283 CGCACATCTCTCAACCTGCG 61.690 60.000 0.00 0.00 41.21 5.18
2039 2141 2.032071 CTGCGGAAAGGACGGGTT 59.968 61.111 0.00 0.00 0.00 4.11
2049 2151 2.625823 GGACGGGTTGACGACGGTA 61.626 63.158 0.00 0.00 37.61 4.02
2051 2153 0.799534 GACGGGTTGACGACGGTATG 60.800 60.000 0.00 0.00 37.61 2.39
2109 2211 3.204505 GGTGACGATGACGGTGAAA 57.795 52.632 0.00 0.00 44.46 2.69
2143 2245 2.719531 TTACCACCAGACTGTTTGCA 57.280 45.000 0.93 0.00 0.00 4.08
2144 2246 2.949177 TACCACCAGACTGTTTGCAT 57.051 45.000 0.93 0.00 0.00 3.96
2145 2247 2.949177 ACCACCAGACTGTTTGCATA 57.051 45.000 0.93 0.00 0.00 3.14
2146 2248 3.439857 ACCACCAGACTGTTTGCATAT 57.560 42.857 0.93 0.00 0.00 1.78
2147 2249 4.568072 ACCACCAGACTGTTTGCATATA 57.432 40.909 0.93 0.00 0.00 0.86
2148 2250 4.517285 ACCACCAGACTGTTTGCATATAG 58.483 43.478 0.93 0.00 0.00 1.31
2149 2251 4.225042 ACCACCAGACTGTTTGCATATAGA 59.775 41.667 7.86 0.00 0.00 1.98
2150 2252 5.185454 CCACCAGACTGTTTGCATATAGAA 58.815 41.667 7.86 0.00 0.00 2.10
2151 2253 5.647658 CCACCAGACTGTTTGCATATAGAAA 59.352 40.000 7.86 0.00 0.00 2.52
2152 2254 6.150976 CCACCAGACTGTTTGCATATAGAAAA 59.849 38.462 7.86 0.00 0.00 2.29
2153 2255 7.309133 CCACCAGACTGTTTGCATATAGAAAAA 60.309 37.037 7.86 0.00 0.00 1.94
2171 2273 1.273759 AAAACTACTCCCTCCGTCCC 58.726 55.000 0.00 0.00 0.00 4.46
2172 2274 0.616964 AAACTACTCCCTCCGTCCCC 60.617 60.000 0.00 0.00 0.00 4.81
2173 2275 1.516645 AACTACTCCCTCCGTCCCCT 61.517 60.000 0.00 0.00 0.00 4.79
2174 2276 0.625683 ACTACTCCCTCCGTCCCCTA 60.626 60.000 0.00 0.00 0.00 3.53
2175 2277 0.554792 CTACTCCCTCCGTCCCCTAA 59.445 60.000 0.00 0.00 0.00 2.69
2176 2278 1.147399 CTACTCCCTCCGTCCCCTAAT 59.853 57.143 0.00 0.00 0.00 1.73
2177 2279 1.238615 ACTCCCTCCGTCCCCTAATA 58.761 55.000 0.00 0.00 0.00 0.98
2178 2280 1.793902 ACTCCCTCCGTCCCCTAATAT 59.206 52.381 0.00 0.00 0.00 1.28
2179 2281 2.998910 ACTCCCTCCGTCCCCTAATATA 59.001 50.000 0.00 0.00 0.00 0.86
2180 2282 3.403737 ACTCCCTCCGTCCCCTAATATAA 59.596 47.826 0.00 0.00 0.00 0.98
2181 2283 4.024670 CTCCCTCCGTCCCCTAATATAAG 58.975 52.174 0.00 0.00 0.00 1.73
2182 2284 3.664127 TCCCTCCGTCCCCTAATATAAGA 59.336 47.826 0.00 0.00 0.00 2.10
2183 2285 4.108451 TCCCTCCGTCCCCTAATATAAGAA 59.892 45.833 0.00 0.00 0.00 2.52
2184 2286 4.222366 CCCTCCGTCCCCTAATATAAGAAC 59.778 50.000 0.00 0.00 0.00 3.01
2185 2287 4.082354 CCTCCGTCCCCTAATATAAGAACG 60.082 50.000 0.00 0.00 0.00 3.95
2186 2288 4.473444 TCCGTCCCCTAATATAAGAACGT 58.527 43.478 0.00 0.00 0.00 3.99
2187 2289 4.895297 TCCGTCCCCTAATATAAGAACGTT 59.105 41.667 0.00 0.00 0.00 3.99
2188 2290 5.363580 TCCGTCCCCTAATATAAGAACGTTT 59.636 40.000 0.46 0.00 0.00 3.60
2189 2291 6.051074 CCGTCCCCTAATATAAGAACGTTTT 58.949 40.000 0.46 0.00 0.00 2.43
2190 2292 6.539826 CCGTCCCCTAATATAAGAACGTTTTT 59.460 38.462 9.22 9.22 0.00 1.94
2191 2293 7.404203 CGTCCCCTAATATAAGAACGTTTTTG 58.596 38.462 13.87 0.00 0.00 2.44
2192 2294 7.278424 CGTCCCCTAATATAAGAACGTTTTTGA 59.722 37.037 13.87 2.81 0.00 2.69
2193 2295 8.393366 GTCCCCTAATATAAGAACGTTTTTGAC 58.607 37.037 13.87 5.89 0.00 3.18
2194 2296 8.102047 TCCCCTAATATAAGAACGTTTTTGACA 58.898 33.333 13.87 0.01 0.00 3.58
2195 2297 8.179615 CCCCTAATATAAGAACGTTTTTGACAC 58.820 37.037 13.87 0.00 0.00 3.67
2196 2298 8.943002 CCCTAATATAAGAACGTTTTTGACACT 58.057 33.333 13.87 0.00 0.00 3.55
2197 2299 9.755064 CCTAATATAAGAACGTTTTTGACACTG 57.245 33.333 13.87 1.56 0.00 3.66
2200 2302 4.759516 AAGAACGTTTTTGACACTGTGT 57.240 36.364 14.23 14.23 0.00 3.72
2201 2303 4.759516 AGAACGTTTTTGACACTGTGTT 57.240 36.364 15.54 0.00 0.00 3.32
2202 2304 4.719040 AGAACGTTTTTGACACTGTGTTC 58.281 39.130 15.54 8.88 35.82 3.18
2203 2305 3.481112 ACGTTTTTGACACTGTGTTCC 57.519 42.857 15.54 3.75 0.00 3.62
2204 2306 2.814919 ACGTTTTTGACACTGTGTTCCA 59.185 40.909 15.54 6.56 0.00 3.53
2205 2307 3.442273 ACGTTTTTGACACTGTGTTCCAT 59.558 39.130 15.54 0.00 0.00 3.41
2206 2308 4.636648 ACGTTTTTGACACTGTGTTCCATA 59.363 37.500 15.54 2.03 0.00 2.74
2207 2309 5.124138 ACGTTTTTGACACTGTGTTCCATAA 59.876 36.000 15.54 7.95 0.00 1.90
2208 2310 6.183360 ACGTTTTTGACACTGTGTTCCATAAT 60.183 34.615 15.54 0.00 0.00 1.28
2209 2311 7.012515 ACGTTTTTGACACTGTGTTCCATAATA 59.987 33.333 15.54 0.00 0.00 0.98
2210 2312 8.020819 CGTTTTTGACACTGTGTTCCATAATAT 58.979 33.333 15.54 0.00 0.00 1.28
2214 2316 9.952030 TTTGACACTGTGTTCCATAATATAAGA 57.048 29.630 15.54 0.00 0.00 2.10
2215 2317 9.952030 TTGACACTGTGTTCCATAATATAAGAA 57.048 29.630 15.54 0.00 0.00 2.52
2216 2318 9.378551 TGACACTGTGTTCCATAATATAAGAAC 57.621 33.333 15.54 7.86 39.22 3.01
2217 2319 8.420374 ACACTGTGTTCCATAATATAAGAACG 57.580 34.615 7.80 0.00 41.17 3.95
2218 2320 8.038944 ACACTGTGTTCCATAATATAAGAACGT 58.961 33.333 7.80 0.00 41.17 3.99
2219 2321 8.879759 CACTGTGTTCCATAATATAAGAACGTT 58.120 33.333 0.00 0.00 41.17 3.99
2220 2322 9.444600 ACTGTGTTCCATAATATAAGAACGTTT 57.555 29.630 0.46 0.00 41.17 3.60
2233 2335 5.405331 AAGAACGTTTTTGACACTAGAGC 57.595 39.130 0.46 0.00 0.00 4.09
2234 2336 4.439057 AGAACGTTTTTGACACTAGAGCA 58.561 39.130 0.46 0.00 0.00 4.26
2235 2337 4.508124 AGAACGTTTTTGACACTAGAGCAG 59.492 41.667 0.46 0.00 0.00 4.24
2236 2338 3.793559 ACGTTTTTGACACTAGAGCAGT 58.206 40.909 0.00 0.00 38.32 4.40
2249 2351 6.305693 ACTAGAGCAGTGTCAAAAATGTTC 57.694 37.500 0.00 0.00 35.62 3.18
2250 2352 6.058183 ACTAGAGCAGTGTCAAAAATGTTCT 58.942 36.000 0.00 0.00 35.62 3.01
2251 2353 5.841957 AGAGCAGTGTCAAAAATGTTCTT 57.158 34.783 0.00 0.00 30.23 2.52
2252 2354 6.942532 AGAGCAGTGTCAAAAATGTTCTTA 57.057 33.333 0.00 0.00 30.23 2.10
2253 2355 7.516198 AGAGCAGTGTCAAAAATGTTCTTAT 57.484 32.000 0.00 0.00 30.23 1.73
2254 2356 8.621532 AGAGCAGTGTCAAAAATGTTCTTATA 57.378 30.769 0.00 0.00 30.23 0.98
2255 2357 9.236006 AGAGCAGTGTCAAAAATGTTCTTATAT 57.764 29.630 0.00 0.00 30.23 0.86
2256 2358 9.846248 GAGCAGTGTCAAAAATGTTCTTATATT 57.154 29.630 0.00 0.00 0.00 1.28
2265 2367 9.677567 CAAAAATGTTCTTATATTATGGGACGG 57.322 33.333 0.00 0.00 0.00 4.79
2266 2368 9.635404 AAAAATGTTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
2267 2369 8.848474 AAATGTTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
2268 2370 6.354794 TGTTCTTATATTATGGGACGGAGG 57.645 41.667 0.00 0.00 0.00 4.30
2269 2371 5.247564 TGTTCTTATATTATGGGACGGAGGG 59.752 44.000 0.00 0.00 0.00 4.30
2270 2372 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2271 2373 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2272 2374 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2273 2375 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2274 2376 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2275 2377 0.186873 TATGGGACGGAGGGAGTACC 59.813 60.000 0.00 0.00 42.94 3.34
2276 2378 2.361771 GGGACGGAGGGAGTACCA 59.638 66.667 0.00 0.00 42.20 3.25
2287 2389 3.034635 AGGGAGTACCACATTAGAGCAG 58.965 50.000 0.00 0.00 43.89 4.24
2319 2422 1.250154 TTGCAAATTCGGCCCCTCAG 61.250 55.000 0.00 0.00 0.00 3.35
2387 2500 2.232756 TGCGCCGTACATTCACATAT 57.767 45.000 4.18 0.00 0.00 1.78
2411 2525 4.604976 GCAAATTCCGATCCTCAAATCTG 58.395 43.478 0.00 0.00 0.00 2.90
2425 2539 5.125900 CCTCAAATCTGTGTAATCCATGCAA 59.874 40.000 0.00 0.00 0.00 4.08
2441 2556 5.105063 CCATGCAAGTCGATCATACGATAT 58.895 41.667 0.00 0.00 43.93 1.63
2490 2607 9.667989 GAAACAAAGCAAAGCAAATCATAATTT 57.332 25.926 0.00 0.00 35.43 1.82
2677 2819 4.547367 GCCCTTGCCGCCTCGTAT 62.547 66.667 0.00 0.00 0.00 3.06
2700 2843 1.202268 CCTACGGTCGTTGATCTCCAC 60.202 57.143 0.16 0.00 0.00 4.02
2743 2891 7.494952 CACTTCTTTGAATGCTCATCATAGAGA 59.505 37.037 0.00 0.00 36.62 3.10
2750 2898 3.145286 TGCTCATCATAGAGAGTCTCGG 58.855 50.000 14.47 8.58 37.87 4.63
2819 2967 3.243839 CCTCTCCTTCTCAAGCTCTATGC 60.244 52.174 0.00 0.00 43.29 3.14
2860 3008 0.531532 CGAGCTCCCATTTGATCGCT 60.532 55.000 8.47 0.00 35.42 4.93
2875 3023 0.532640 TCGCTGCTTGTTGCTTCTCA 60.533 50.000 0.00 0.00 43.37 3.27
2902 3050 4.711846 TCGATCTTCTCCCTCTCAATTTCA 59.288 41.667 0.00 0.00 0.00 2.69
2934 3082 2.660064 CCCTCTTCCGGTCCCACTG 61.660 68.421 0.00 0.00 0.00 3.66
2937 3085 2.358737 CTTCCGGTCCCACTGCAC 60.359 66.667 0.00 0.00 0.00 4.57
2960 3109 0.313672 TTCCTTTGCGCATCCAACAC 59.686 50.000 12.75 0.00 0.00 3.32
3082 3238 2.162681 CCCACTTGTTTCCCATGACTC 58.837 52.381 0.00 0.00 0.00 3.36
3083 3239 2.162681 CCACTTGTTTCCCATGACTCC 58.837 52.381 0.00 0.00 0.00 3.85
3088 3244 3.969250 TTTCCCATGACTCCGCGGC 62.969 63.158 23.51 7.40 0.00 6.53
3090 3246 4.552365 CCCATGACTCCGCGGCAT 62.552 66.667 23.51 16.01 0.00 4.40
3091 3247 2.969238 CCATGACTCCGCGGCATC 60.969 66.667 23.51 20.46 0.00 3.91
3092 3248 2.202919 CATGACTCCGCGGCATCA 60.203 61.111 26.74 26.74 0.00 3.07
3093 3249 2.202932 ATGACTCCGCGGCATCAC 60.203 61.111 26.99 14.67 0.00 3.06
3094 3250 4.794439 TGACTCCGCGGCATCACG 62.794 66.667 23.51 6.56 0.00 4.35
3116 3272 3.050275 GCACGTGCCTTCTCCCAC 61.050 66.667 30.12 0.00 34.31 4.61
3117 3273 2.743718 CACGTGCCTTCTCCCACT 59.256 61.111 0.82 0.00 0.00 4.00
3118 3274 1.071471 CACGTGCCTTCTCCCACTT 59.929 57.895 0.82 0.00 0.00 3.16
3119 3275 1.071471 ACGTGCCTTCTCCCACTTG 59.929 57.895 0.00 0.00 0.00 3.16
3120 3276 1.071471 CGTGCCTTCTCCCACTTGT 59.929 57.895 0.00 0.00 0.00 3.16
3121 3277 0.535102 CGTGCCTTCTCCCACTTGTT 60.535 55.000 0.00 0.00 0.00 2.83
3122 3278 1.692411 GTGCCTTCTCCCACTTGTTT 58.308 50.000 0.00 0.00 0.00 2.83
3123 3279 1.609072 GTGCCTTCTCCCACTTGTTTC 59.391 52.381 0.00 0.00 0.00 2.78
3124 3280 1.248486 GCCTTCTCCCACTTGTTTCC 58.752 55.000 0.00 0.00 0.00 3.13
3125 3281 1.911057 CCTTCTCCCACTTGTTTCCC 58.089 55.000 0.00 0.00 0.00 3.97
3126 3282 1.144913 CCTTCTCCCACTTGTTTCCCA 59.855 52.381 0.00 0.00 0.00 4.37
3127 3283 2.225117 CCTTCTCCCACTTGTTTCCCAT 60.225 50.000 0.00 0.00 0.00 4.00
3128 3284 2.584835 TCTCCCACTTGTTTCCCATG 57.415 50.000 0.00 0.00 0.00 3.66
3129 3285 2.061848 TCTCCCACTTGTTTCCCATGA 58.938 47.619 0.00 0.00 0.00 3.07
3130 3286 2.162681 CTCCCACTTGTTTCCCATGAC 58.837 52.381 0.00 0.00 0.00 3.06
3131 3287 1.780309 TCCCACTTGTTTCCCATGACT 59.220 47.619 0.00 0.00 0.00 3.41
3132 3288 2.176798 TCCCACTTGTTTCCCATGACTT 59.823 45.455 0.00 0.00 0.00 3.01
3133 3289 2.297033 CCCACTTGTTTCCCATGACTTG 59.703 50.000 0.00 0.00 0.00 3.16
3134 3290 2.297033 CCACTTGTTTCCCATGACTTGG 59.703 50.000 0.00 0.22 46.00 3.61
3135 3291 1.963515 ACTTGTTTCCCATGACTTGGC 59.036 47.619 0.00 0.00 44.97 4.52
3136 3292 0.958091 TTGTTTCCCATGACTTGGCG 59.042 50.000 0.00 0.00 44.97 5.69
3137 3293 0.893270 TGTTTCCCATGACTTGGCGG 60.893 55.000 0.00 0.00 44.97 6.13
3138 3294 0.893727 GTTTCCCATGACTTGGCGGT 60.894 55.000 0.00 0.00 44.97 5.68
3139 3295 0.178975 TTTCCCATGACTTGGCGGTT 60.179 50.000 0.00 0.00 44.97 4.44
3140 3296 0.893270 TTCCCATGACTTGGCGGTTG 60.893 55.000 0.00 0.00 44.97 3.77
3141 3297 1.603455 CCCATGACTTGGCGGTTGT 60.603 57.895 0.00 0.00 44.97 3.32
3142 3298 1.586154 CCCATGACTTGGCGGTTGTC 61.586 60.000 0.00 0.00 44.97 3.18
3143 3299 1.586154 CCATGACTTGGCGGTTGTCC 61.586 60.000 0.00 0.00 39.09 4.02
3144 3300 0.606401 CATGACTTGGCGGTTGTCCT 60.606 55.000 0.00 0.00 0.00 3.85
3145 3301 0.110486 ATGACTTGGCGGTTGTCCTT 59.890 50.000 0.00 0.00 0.00 3.36
3146 3302 0.106918 TGACTTGGCGGTTGTCCTTT 60.107 50.000 0.00 0.00 0.00 3.11
3147 3303 0.310854 GACTTGGCGGTTGTCCTTTG 59.689 55.000 0.00 0.00 0.00 2.77
3148 3304 1.106944 ACTTGGCGGTTGTCCTTTGG 61.107 55.000 0.00 0.00 0.00 3.28
3149 3305 2.420466 CTTGGCGGTTGTCCTTTGGC 62.420 60.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.601546 TGATAGGGCATGTACAATATACAATGA 58.398 33.333 0.00 0.00 0.00 2.57
1 2 8.791327 TGATAGGGCATGTACAATATACAATG 57.209 34.615 0.00 0.00 0.00 2.82
7 8 7.872993 GCGTATATGATAGGGCATGTACAATAT 59.127 37.037 0.00 0.00 40.65 1.28
8 9 7.147811 TGCGTATATGATAGGGCATGTACAATA 60.148 37.037 0.00 0.00 40.65 1.90
9 10 6.049149 GCGTATATGATAGGGCATGTACAAT 58.951 40.000 0.00 0.00 40.65 2.71
65 66 1.269257 GCGTGGTCTGATGATGATCGA 60.269 52.381 0.00 0.00 0.00 3.59
67 68 1.863454 GTGCGTGGTCTGATGATGATC 59.137 52.381 0.00 0.00 0.00 2.92
68 69 1.473965 GGTGCGTGGTCTGATGATGAT 60.474 52.381 0.00 0.00 0.00 2.45
71 72 0.107993 CAGGTGCGTGGTCTGATGAT 60.108 55.000 0.00 0.00 0.00 2.45
155 156 1.445582 GGAGTCCTGGTTACGCGTG 60.446 63.158 24.59 3.89 0.00 5.34
233 234 1.657822 TCAGAGACCGAGAGACATCG 58.342 55.000 0.00 0.00 42.36 3.84
296 299 2.512515 GCGCTGTGGGAAGGCTAG 60.513 66.667 0.00 0.00 0.00 3.42
499 508 2.408241 CCGGTCCGTGTCTCTCTCC 61.408 68.421 11.06 0.00 0.00 3.71
673 702 3.604667 CTTGCGGCAACTTGGGCA 61.605 61.111 12.11 0.00 0.00 5.36
689 718 1.900016 CTGCATGTGGTGTGTGGCT 60.900 57.895 0.00 0.00 0.00 4.75
706 735 1.079266 CTCTGCTTTGCTCCTCGCT 60.079 57.895 0.00 0.00 40.11 4.93
754 783 3.483421 CAGGATGGAATAGCTGCATTCA 58.517 45.455 19.19 5.64 35.99 2.57
859 896 4.208746 GCGTATATATAGGGCTCTGGAGT 58.791 47.826 13.00 0.00 0.00 3.85
860 897 4.036971 GTGCGTATATATAGGGCTCTGGAG 59.963 50.000 13.00 0.00 0.00 3.86
868 905 4.440250 GGTGAGCTGTGCGTATATATAGGG 60.440 50.000 13.00 1.46 0.00 3.53
910 948 2.092681 CGACGGATGGATGAATAATGCG 59.907 50.000 0.00 0.00 40.46 4.73
929 967 2.954611 CTCTGTGTCGGCTGTCGA 59.045 61.111 0.00 0.00 46.77 4.20
988 1050 1.664649 GCGCCATCGATCGAATGGA 60.665 57.895 32.55 12.12 37.66 3.41
1181 1244 0.389948 GTTGGAGATCGAACGCAGGT 60.390 55.000 0.00 0.00 0.00 4.00
1255 1318 3.044305 GTGGTGGAGCTGTGACGC 61.044 66.667 0.00 0.00 0.00 5.19
1260 1323 3.399105 TTGCACGTGGTGGAGCTGT 62.399 57.895 18.88 0.00 34.96 4.40
1280 1343 3.614092 TCTCGAAACGTATACTCCTGGT 58.386 45.455 0.56 0.00 0.00 4.00
1285 1348 3.311871 TCCTGCTCTCGAAACGTATACTC 59.688 47.826 0.56 0.00 0.00 2.59
1287 1350 3.548415 CCTCCTGCTCTCGAAACGTATAC 60.548 52.174 0.00 0.00 0.00 1.47
1294 1363 0.809385 CGTACCTCCTGCTCTCGAAA 59.191 55.000 0.00 0.00 0.00 3.46
1296 1365 1.451567 CCGTACCTCCTGCTCTCGA 60.452 63.158 0.00 0.00 0.00 4.04
1298 1367 1.076923 TCCCGTACCTCCTGCTCTC 60.077 63.158 0.00 0.00 0.00 3.20
1305 1374 2.424733 GCTCACCTCCCGTACCTCC 61.425 68.421 0.00 0.00 0.00 4.30
1308 1377 2.722201 CCTGCTCACCTCCCGTACC 61.722 68.421 0.00 0.00 0.00 3.34
1310 1379 0.554305 TATCCTGCTCACCTCCCGTA 59.446 55.000 0.00 0.00 0.00 4.02
1350 1419 1.066787 ACTACAGCTTCTTCTTCGGCC 60.067 52.381 0.00 0.00 0.00 6.13
1354 1423 1.996191 CGCCACTACAGCTTCTTCTTC 59.004 52.381 0.00 0.00 0.00 2.87
1451 1520 1.137614 GCGACTGATGCTGACTCGA 59.862 57.895 0.00 0.00 0.00 4.04
1456 1525 1.078918 CTTGGGCGACTGATGCTGA 60.079 57.895 0.00 0.00 0.00 4.26
1558 1627 4.083862 GGCTTCGACCTCGCCCTT 62.084 66.667 3.52 0.00 37.86 3.95
1574 1643 0.179089 CAAGCTGATGGACTCCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
1577 1646 3.406442 TCCAAGCTGATGGACTCCT 57.594 52.632 2.82 0.00 44.52 3.69
1776 1863 0.404040 GGGTGTGGTTGAGGATGGAA 59.596 55.000 0.00 0.00 0.00 3.53
1849 1941 2.159612 TCTACACGATCAAACGAGACGG 60.160 50.000 0.00 0.00 37.03 4.79
1953 2046 6.325028 TCTCTCTGCCTGCTAGTATAAAACAT 59.675 38.462 0.00 0.00 0.00 2.71
1954 2047 5.656859 TCTCTCTGCCTGCTAGTATAAAACA 59.343 40.000 0.00 0.00 0.00 2.83
1955 2048 6.150396 TCTCTCTGCCTGCTAGTATAAAAC 57.850 41.667 0.00 0.00 0.00 2.43
1958 2051 5.300539 CAGTTCTCTCTGCCTGCTAGTATAA 59.699 44.000 0.00 0.00 0.00 0.98
1998 2100 0.104487 AGAGATGTGCGATCTGCCAG 59.896 55.000 2.87 0.00 45.60 4.85
2000 2102 0.103755 TGAGAGATGTGCGATCTGCC 59.896 55.000 2.87 0.00 45.60 4.85
2007 2109 1.690283 CGCAGGTTGAGAGATGTGCG 61.690 60.000 0.00 0.00 46.50 5.34
2026 2128 0.947660 GTCGTCAACCCGTCCTTTCC 60.948 60.000 0.00 0.00 0.00 3.13
2039 2141 1.881973 GGTATAGCCATACCGTCGTCA 59.118 52.381 5.53 0.00 45.60 4.35
2049 2151 1.722011 GCGTATTGCGGTATAGCCAT 58.278 50.000 0.00 0.00 41.69 4.40
2109 2211 2.679336 GTGGTAAATCAATTACGCCGGT 59.321 45.455 1.90 0.00 44.06 5.28
2123 2225 3.006112 TGCAAACAGTCTGGTGGTAAA 57.994 42.857 4.53 0.00 0.00 2.01
2151 2253 1.627329 GGGACGGAGGGAGTAGTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
2152 2254 1.273759 GGGACGGAGGGAGTAGTTTT 58.726 55.000 0.00 0.00 0.00 2.43
2153 2255 0.616964 GGGGACGGAGGGAGTAGTTT 60.617 60.000 0.00 0.00 0.00 2.66
2154 2256 1.001376 GGGGACGGAGGGAGTAGTT 59.999 63.158 0.00 0.00 0.00 2.24
2155 2257 0.625683 TAGGGGACGGAGGGAGTAGT 60.626 60.000 0.00 0.00 0.00 2.73
2156 2258 0.554792 TTAGGGGACGGAGGGAGTAG 59.445 60.000 0.00 0.00 0.00 2.57
2157 2259 1.238615 ATTAGGGGACGGAGGGAGTA 58.761 55.000 0.00 0.00 0.00 2.59
2158 2260 1.238615 TATTAGGGGACGGAGGGAGT 58.761 55.000 0.00 0.00 0.00 3.85
2159 2261 2.625282 ATATTAGGGGACGGAGGGAG 57.375 55.000 0.00 0.00 0.00 4.30
2160 2262 3.664127 TCTTATATTAGGGGACGGAGGGA 59.336 47.826 0.00 0.00 0.00 4.20
2161 2263 4.057063 TCTTATATTAGGGGACGGAGGG 57.943 50.000 0.00 0.00 0.00 4.30
2162 2264 4.082354 CGTTCTTATATTAGGGGACGGAGG 60.082 50.000 0.00 0.00 0.00 4.30
2163 2265 4.522022 ACGTTCTTATATTAGGGGACGGAG 59.478 45.833 13.52 0.00 0.00 4.63
2164 2266 4.473444 ACGTTCTTATATTAGGGGACGGA 58.527 43.478 13.52 0.00 0.00 4.69
2165 2267 4.861102 ACGTTCTTATATTAGGGGACGG 57.139 45.455 13.52 0.00 0.00 4.79
2166 2268 7.278424 TCAAAAACGTTCTTATATTAGGGGACG 59.722 37.037 0.00 9.81 0.00 4.79
2167 2269 8.393366 GTCAAAAACGTTCTTATATTAGGGGAC 58.607 37.037 0.00 0.00 0.00 4.46
2168 2270 8.102047 TGTCAAAAACGTTCTTATATTAGGGGA 58.898 33.333 0.00 0.00 0.00 4.81
2169 2271 8.179615 GTGTCAAAAACGTTCTTATATTAGGGG 58.820 37.037 0.00 0.00 0.00 4.79
2170 2272 8.943002 AGTGTCAAAAACGTTCTTATATTAGGG 58.057 33.333 0.00 0.00 0.00 3.53
2171 2273 9.755064 CAGTGTCAAAAACGTTCTTATATTAGG 57.245 33.333 0.00 0.00 0.00 2.69
2174 2276 8.617809 ACACAGTGTCAAAAACGTTCTTATATT 58.382 29.630 0.00 0.00 0.00 1.28
2175 2277 8.149973 ACACAGTGTCAAAAACGTTCTTATAT 57.850 30.769 0.00 0.00 0.00 0.86
2176 2278 7.542534 ACACAGTGTCAAAAACGTTCTTATA 57.457 32.000 0.00 0.00 0.00 0.98
2177 2279 6.431198 ACACAGTGTCAAAAACGTTCTTAT 57.569 33.333 0.00 0.00 0.00 1.73
2178 2280 5.866335 ACACAGTGTCAAAAACGTTCTTA 57.134 34.783 0.00 0.00 0.00 2.10
2179 2281 4.759516 ACACAGTGTCAAAAACGTTCTT 57.240 36.364 0.00 0.00 0.00 2.52
2180 2282 4.379082 GGAACACAGTGTCAAAAACGTTCT 60.379 41.667 6.67 0.00 33.67 3.01
2181 2283 3.849708 GGAACACAGTGTCAAAAACGTTC 59.150 43.478 6.67 10.41 0.00 3.95
2182 2284 3.253677 TGGAACACAGTGTCAAAAACGTT 59.746 39.130 6.67 0.00 0.00 3.99
2183 2285 2.814919 TGGAACACAGTGTCAAAAACGT 59.185 40.909 6.67 0.00 0.00 3.99
2184 2286 3.479505 TGGAACACAGTGTCAAAAACG 57.520 42.857 6.67 0.00 0.00 3.60
2207 2309 8.870879 GCTCTAGTGTCAAAAACGTTCTTATAT 58.129 33.333 0.00 0.00 0.00 0.86
2208 2310 7.868922 TGCTCTAGTGTCAAAAACGTTCTTATA 59.131 33.333 0.00 0.00 0.00 0.98
2209 2311 6.704493 TGCTCTAGTGTCAAAAACGTTCTTAT 59.296 34.615 0.00 0.00 0.00 1.73
2210 2312 6.044046 TGCTCTAGTGTCAAAAACGTTCTTA 58.956 36.000 0.00 0.00 0.00 2.10
2211 2313 4.873827 TGCTCTAGTGTCAAAAACGTTCTT 59.126 37.500 0.00 0.00 0.00 2.52
2212 2314 4.439057 TGCTCTAGTGTCAAAAACGTTCT 58.561 39.130 0.00 0.00 0.00 3.01
2213 2315 4.270325 ACTGCTCTAGTGTCAAAAACGTTC 59.730 41.667 0.00 0.00 38.49 3.95
2214 2316 4.189231 ACTGCTCTAGTGTCAAAAACGTT 58.811 39.130 0.00 0.00 38.49 3.99
2215 2317 3.793559 ACTGCTCTAGTGTCAAAAACGT 58.206 40.909 0.00 0.00 38.49 3.99
2226 2328 6.058183 AGAACATTTTTGACACTGCTCTAGT 58.942 36.000 0.00 0.00 41.36 2.57
2227 2329 6.551385 AGAACATTTTTGACACTGCTCTAG 57.449 37.500 0.00 0.00 0.00 2.43
2228 2330 6.942532 AAGAACATTTTTGACACTGCTCTA 57.057 33.333 0.00 0.00 0.00 2.43
2229 2331 5.841957 AAGAACATTTTTGACACTGCTCT 57.158 34.783 0.00 0.00 0.00 4.09
2230 2332 9.846248 AATATAAGAACATTTTTGACACTGCTC 57.154 29.630 0.00 0.00 0.00 4.26
2239 2341 9.677567 CCGTCCCATAATATAAGAACATTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
2240 2342 9.635404 TCCGTCCCATAATATAAGAACATTTTT 57.365 29.630 0.00 0.00 0.00 1.94
2241 2343 9.284968 CTCCGTCCCATAATATAAGAACATTTT 57.715 33.333 0.00 0.00 0.00 1.82
2242 2344 7.883311 CCTCCGTCCCATAATATAAGAACATTT 59.117 37.037 0.00 0.00 0.00 2.32
2243 2345 7.394816 CCTCCGTCCCATAATATAAGAACATT 58.605 38.462 0.00 0.00 0.00 2.71
2244 2346 6.070194 CCCTCCGTCCCATAATATAAGAACAT 60.070 42.308 0.00 0.00 0.00 2.71
2245 2347 5.247564 CCCTCCGTCCCATAATATAAGAACA 59.752 44.000 0.00 0.00 0.00 3.18
2246 2348 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2247 2349 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2248 2350 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2249 2351 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2250 2352 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2251 2353 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2252 2354 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2253 2355 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
2254 2356 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
2255 2357 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
2256 2358 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
2257 2359 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
2258 2360 2.361771 GGTACTCCCTCCGTCCCA 59.638 66.667 0.00 0.00 0.00 4.37
2259 2361 2.056815 GTGGTACTCCCTCCGTCCC 61.057 68.421 0.00 0.00 0.00 4.46
2260 2362 0.686769 ATGTGGTACTCCCTCCGTCC 60.687 60.000 0.00 0.00 0.00 4.79
2261 2363 1.192428 AATGTGGTACTCCCTCCGTC 58.808 55.000 0.00 0.00 0.00 4.79
2262 2364 2.024655 TCTAATGTGGTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
2263 2365 2.623889 CTCTAATGTGGTACTCCCTCCG 59.376 54.545 0.00 0.00 0.00 4.63
2264 2366 2.365941 GCTCTAATGTGGTACTCCCTCC 59.634 54.545 0.00 0.00 0.00 4.30
2265 2367 3.031736 TGCTCTAATGTGGTACTCCCTC 58.968 50.000 0.00 0.00 0.00 4.30
2266 2368 3.034635 CTGCTCTAATGTGGTACTCCCT 58.965 50.000 0.00 0.00 0.00 4.20
2267 2369 2.483889 GCTGCTCTAATGTGGTACTCCC 60.484 54.545 0.00 0.00 0.00 4.30
2268 2370 2.432510 AGCTGCTCTAATGTGGTACTCC 59.567 50.000 0.00 0.00 0.00 3.85
2269 2371 3.810310 AGCTGCTCTAATGTGGTACTC 57.190 47.619 0.00 0.00 0.00 2.59
2270 2372 4.023980 TGTAGCTGCTCTAATGTGGTACT 58.976 43.478 4.91 0.00 34.13 2.73
2271 2373 4.142138 ACTGTAGCTGCTCTAATGTGGTAC 60.142 45.833 4.91 0.00 33.76 3.34
2272 2374 4.023980 ACTGTAGCTGCTCTAATGTGGTA 58.976 43.478 4.91 0.00 0.00 3.25
2273 2375 2.834549 ACTGTAGCTGCTCTAATGTGGT 59.165 45.455 4.91 0.00 0.00 4.16
2274 2376 3.452474 GACTGTAGCTGCTCTAATGTGG 58.548 50.000 4.91 0.00 0.00 4.17
2275 2377 3.111838 CGACTGTAGCTGCTCTAATGTG 58.888 50.000 4.91 0.00 0.00 3.21
2276 2378 2.099921 CCGACTGTAGCTGCTCTAATGT 59.900 50.000 4.91 0.00 0.00 2.71
2287 2389 1.508632 TTTGCAAGTCCGACTGTAGC 58.491 50.000 0.65 7.75 0.00 3.58
2350 2463 1.993956 CAACATTTGAGGGGTGTCCA 58.006 50.000 0.00 0.00 38.24 4.02
2387 2500 2.394930 TTGAGGATCGGAATTTGCGA 57.605 45.000 15.38 15.38 45.91 5.10
2411 2525 3.871006 TGATCGACTTGCATGGATTACAC 59.129 43.478 4.44 0.00 0.00 2.90
2425 2539 8.231161 CAGACAGTTTATATCGTATGATCGACT 58.769 37.037 0.00 0.00 42.56 4.18
2441 2556 4.213270 CGAACTTTGGCATCAGACAGTTTA 59.787 41.667 1.42 0.00 31.60 2.01
2490 2607 5.240403 TCATTTTGTCATGTCCGATTTGTCA 59.760 36.000 0.00 0.00 0.00 3.58
2491 2608 5.698832 TCATTTTGTCATGTCCGATTTGTC 58.301 37.500 0.00 0.00 0.00 3.18
2497 2614 5.956068 TGATTTCATTTTGTCATGTCCGA 57.044 34.783 0.00 0.00 0.00 4.55
2665 2807 0.103572 GTAGGAAATACGAGGCGGCA 59.896 55.000 13.08 0.00 0.00 5.69
2743 2891 3.706373 ATGTTGGCGGCCGAGACT 61.706 61.111 33.48 10.23 0.00 3.24
2750 2898 2.537560 CGAGGATCATGTTGGCGGC 61.538 63.158 0.00 0.00 33.17 6.53
2875 3023 3.702792 TGAGAGGGAGAAGATCGAGTTT 58.297 45.455 0.00 0.00 0.00 2.66
2902 3050 1.655372 AGAGGGCAGAGAAGAAGCTT 58.345 50.000 0.00 0.00 0.00 3.74
2934 3082 0.390209 ATGCGCAAAGGAAATGGTGC 60.390 50.000 17.11 0.00 37.29 5.01
2937 3085 0.531657 TGGATGCGCAAAGGAAATGG 59.468 50.000 17.11 0.00 0.00 3.16
2960 3109 0.741915 GGAGGAGAGGTACAAGCTCG 59.258 60.000 0.00 0.00 46.62 5.03
3026 3182 2.954868 GTGATGCCGCGTCTACCG 60.955 66.667 13.67 0.00 40.40 4.02
3099 3255 3.050275 GTGGGAGAAGGCACGTGC 61.050 66.667 32.15 32.15 41.14 5.34
3100 3256 1.071471 AAGTGGGAGAAGGCACGTG 59.929 57.895 12.28 12.28 0.00 4.49
3101 3257 1.071471 CAAGTGGGAGAAGGCACGT 59.929 57.895 0.00 0.00 0.00 4.49
3102 3258 0.535102 AACAAGTGGGAGAAGGCACG 60.535 55.000 0.00 0.00 0.00 5.34
3103 3259 1.609072 GAAACAAGTGGGAGAAGGCAC 59.391 52.381 0.00 0.00 0.00 5.01
3104 3260 1.478654 GGAAACAAGTGGGAGAAGGCA 60.479 52.381 0.00 0.00 0.00 4.75
3105 3261 1.248486 GGAAACAAGTGGGAGAAGGC 58.752 55.000 0.00 0.00 0.00 4.35
3106 3262 1.144913 TGGGAAACAAGTGGGAGAAGG 59.855 52.381 0.00 0.00 0.00 3.46
3107 3263 2.656947 TGGGAAACAAGTGGGAGAAG 57.343 50.000 0.00 0.00 0.00 2.85
3108 3264 2.445145 TCATGGGAAACAAGTGGGAGAA 59.555 45.455 0.00 0.00 0.00 2.87
3109 3265 2.061848 TCATGGGAAACAAGTGGGAGA 58.938 47.619 0.00 0.00 0.00 3.71
3110 3266 2.162681 GTCATGGGAAACAAGTGGGAG 58.837 52.381 0.00 0.00 0.00 4.30
3111 3267 1.780309 AGTCATGGGAAACAAGTGGGA 59.220 47.619 0.00 0.00 0.00 4.37
3112 3268 2.292828 AGTCATGGGAAACAAGTGGG 57.707 50.000 0.00 0.00 0.00 4.61
3113 3269 2.297033 CCAAGTCATGGGAAACAAGTGG 59.703 50.000 0.00 0.00 46.27 4.00
3114 3270 3.648339 CCAAGTCATGGGAAACAAGTG 57.352 47.619 0.00 0.00 46.27 3.16
3125 3281 0.606401 AGGACAACCGCCAAGTCATG 60.606 55.000 0.00 0.00 41.83 3.07
3126 3282 0.110486 AAGGACAACCGCCAAGTCAT 59.890 50.000 0.00 0.00 41.83 3.06
3127 3283 0.106918 AAAGGACAACCGCCAAGTCA 60.107 50.000 0.00 0.00 41.83 3.41
3128 3284 0.310854 CAAAGGACAACCGCCAAGTC 59.689 55.000 0.00 0.00 41.83 3.01
3129 3285 1.106944 CCAAAGGACAACCGCCAAGT 61.107 55.000 0.00 0.00 41.83 3.16
3130 3286 1.659794 CCAAAGGACAACCGCCAAG 59.340 57.895 0.00 0.00 41.83 3.61
3131 3287 2.494530 GCCAAAGGACAACCGCCAA 61.495 57.895 0.00 0.00 41.83 4.52
3132 3288 2.909965 GCCAAAGGACAACCGCCA 60.910 61.111 0.00 0.00 41.83 5.69


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

AutoCloner maintained by Alex Coulton.