Multiple sequence alignment - TraesCS2D01G089400

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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 TraesCS2D01G089400 chr2D 100.000 2567 0 0 1 2567 39438765 39436199 0.000000e+00 4741.0
1 TraesCS2D01G089400 chr2D 93.182 1672 101 6 1 1670 55404651 55406311 0.000000e+00 2444.0
2 TraesCS2D01G089400 chr2D 93.056 1224 84 1 407 1629 55412664 55413887 0.000000e+00 1788.0
3 TraesCS2D01G089400 chr2D 89.671 1336 107 13 349 1682 55601551 55602857 0.000000e+00 1674.0
4 TraesCS2D01G089400 chr2D 92.993 999 67 3 686 1682 55435562 55436559 0.000000e+00 1454.0
5 TraesCS2D01G089400 chr2D 83.092 207 23 8 1688 1887 55406551 55406752 7.300000e-41 178.0
6 TraesCS2D01G089400 chr2D 90.152 132 13 0 1 132 55410359 55410490 3.400000e-39 172.0
7 TraesCS2D01G089400 chr2D 82.609 207 24 8 1688 1887 55414186 55414387 3.400000e-39 172.0
8 TraesCS2D01G089400 chr2D 90.152 132 13 0 1 132 55418002 55418133 3.400000e-39 172.0
9 TraesCS2D01G089400 chr2D 89.394 132 14 0 1 132 55591817 55591948 1.580000e-37 167.0
10 TraesCS2D01G089400 chr2B 91.646 1221 67 17 1 1219 88187317 88188504 0.000000e+00 1657.0
11 TraesCS2D01G089400 chr2B 89.003 582 48 9 1577 2148 88241558 88242133 0.000000e+00 706.0
12 TraesCS2D01G089400 chr2B 87.681 414 38 4 1731 2136 88236554 88236962 1.080000e-128 470.0
13 TraesCS2D01G089400 chr2B 94.894 235 12 0 1367 1601 88241317 88241551 4.040000e-98 368.0
14 TraesCS2D01G089400 chr2B 97.183 142 3 1 1577 1717 88231610 88231751 3.300000e-59 239.0
15 TraesCS2D01G089400 chr2B 88.119 202 14 3 1408 1601 88231404 88231603 5.520000e-57 231.0
16 TraesCS2D01G089400 chr2B 96.078 51 2 0 1367 1417 88205879 88205929 1.640000e-12 84.2
17 TraesCS2D01G089400 chr2A 94.444 360 20 0 1226 1585 56990606 56990965 2.890000e-154 555.0
18 TraesCS2D01G089400 chr2A 89.295 383 27 2 846 1228 56945368 56945736 3.870000e-128 468.0
19 TraesCS2D01G089400 chr2A 90.777 206 17 2 3 207 56944980 56945184 9.050000e-70 274.0
20 TraesCS2D01G089400 chr2A 90.909 165 15 0 653 817 56945205 56945369 3.320000e-54 222.0
21 TraesCS2D01G089400 chr2A 92.405 158 9 2 1598 1754 57025245 57025400 3.320000e-54 222.0
22 TraesCS2D01G089400 chr2A 79.245 106 14 6 2463 2567 356716814 356716912 1.650000e-07 67.6
23 TraesCS2D01G089400 chr5B 80.751 213 35 4 2359 2567 694301766 694301976 7.350000e-36 161.0
24 TraesCS2D01G089400 chr5D 80.751 213 33 5 2359 2567 77438021 77438229 2.640000e-35 159.0
25 TraesCS2D01G089400 chr7B 77.447 235 41 9 2339 2567 289193378 289193606 2.070000e-26 130.0
26 TraesCS2D01G089400 chr7B 75.847 236 44 9 2339 2564 716381441 716381673 9.710000e-20 108.0
27 TraesCS2D01G089400 chr4A 77.404 208 40 5 2367 2567 708303098 708302891 1.610000e-22 117.0
28 TraesCS2D01G089400 chr3D 92.308 52 2 2 2517 2567 264595613 264595563 3.540000e-09 73.1
29 TraesCS2D01G089400 chrUn 83.784 74 7 3 2498 2567 2483508 2483436 5.930000e-07 65.8
30 TraesCS2D01G089400 chrUn 83.784 74 7 3 2498 2567 336668872 336668944 5.930000e-07 65.8


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 TraesCS2D01G089400 chr2D 39436199 39438765 2566 True 4741.000000 4741 100.000000 1 2567 1 chr2D.!!$R1 2566
1 TraesCS2D01G089400 chr2D 55601551 55602857 1306 False 1674.000000 1674 89.671000 349 1682 1 chr2D.!!$F3 1333
2 TraesCS2D01G089400 chr2D 55435562 55436559 997 False 1454.000000 1454 92.993000 686 1682 1 chr2D.!!$F1 996
3 TraesCS2D01G089400 chr2D 55404651 55418133 13482 False 821.000000 2444 88.707167 1 1887 6 chr2D.!!$F4 1886
4 TraesCS2D01G089400 chr2B 88187317 88188504 1187 False 1657.000000 1657 91.646000 1 1219 1 chr2B.!!$F1 1218
5 TraesCS2D01G089400 chr2B 88241317 88242133 816 False 537.000000 706 91.948500 1367 2148 2 chr2B.!!$F5 781
6 TraesCS2D01G089400 chr2A 56944980 56945736 756 False 321.333333 468 90.327000 3 1228 3 chr2A.!!$F4 1225

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
226 229 0.406361 TGGGGTTCGGGCTTTTGTAT 59.594 50.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 12815 0.034574 TCACACCACACCAAAGCACT 60.035 50.0 0.0 0.0 0.0 4.4 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
118 119 0.599991 GGCATCACGTCTGACACACA 60.600 55.000 8.73 0.00 0.00 3.72
122 123 3.665323 GCATCACGTCTGACACACATTTC 60.665 47.826 8.73 0.00 0.00 2.17
123 124 2.479837 TCACGTCTGACACACATTTCC 58.520 47.619 8.73 0.00 0.00 3.13
176 179 3.244181 GCTTGAGAAAAAGGGGCATTTCA 60.244 43.478 0.00 0.00 37.87 2.69
190 193 2.301583 GCATTTCAGGGCTTTGGGTTAA 59.698 45.455 0.00 0.00 0.00 2.01
226 229 0.406361 TGGGGTTCGGGCTTTTGTAT 59.594 50.000 0.00 0.00 0.00 2.29
268 271 4.825085 TCAGGTTTAGCTTTGGAACGATTT 59.175 37.500 0.00 0.00 0.00 2.17
289 292 3.482436 TGGAAACAAGAATAACACGGCT 58.518 40.909 0.00 0.00 37.44 5.52
382 385 3.196254 GGTTGACAAGTACGAATAGGGGA 59.804 47.826 0.00 0.00 0.00 4.81
399 402 1.524482 GAGATGGGGGAGTCACTGC 59.476 63.158 0.00 0.00 0.00 4.40
436 439 1.369983 AGGGGGTTAGGTGAGATCCTT 59.630 52.381 0.00 0.00 38.86 3.36
694 703 8.651391 TTAATTCCGCAGATTCGTAAAGATAA 57.349 30.769 0.00 0.00 0.00 1.75
773 782 6.855914 TGTGATTTCGTGCATCTAAAACTTTC 59.144 34.615 0.00 0.00 0.00 2.62
897 907 7.892778 TTTATCACGCATTCACACTACTTTA 57.107 32.000 0.00 0.00 0.00 1.85
909 919 5.472137 TCACACTACTTTATTGGTTCTTGGC 59.528 40.000 0.00 0.00 0.00 4.52
985 995 8.954350 AGATTTCACATTTCACATAGAGAAAGG 58.046 33.333 0.00 0.00 41.16 3.11
995 1005 4.154918 CACATAGAGAAAGGCACAGGAAAC 59.845 45.833 0.00 0.00 0.00 2.78
998 1008 2.039084 AGAGAAAGGCACAGGAAACGAT 59.961 45.455 0.00 0.00 0.00 3.73
1012 1022 5.525012 CAGGAAACGATAATGAAGAGCATGA 59.475 40.000 0.00 0.00 37.28 3.07
1038 1048 3.245229 CCACCATATATGCCCTTGCCTTA 60.245 47.826 7.24 0.00 36.33 2.69
1191 1201 3.050619 GCATGCTGCATTTGAGAATAGC 58.949 45.455 13.38 6.23 44.26 2.97
1263 1273 0.827507 AAGAAACCCAGCGCATTGGT 60.828 50.000 11.47 10.24 36.45 3.67
1272 1282 3.380004 CCCAGCGCATTGGTAAGAATTTA 59.620 43.478 11.47 0.00 36.45 1.40
1284 1294 6.013379 TGGTAAGAATTTATTGCAGAACCCA 58.987 36.000 0.00 0.00 0.00 4.51
1318 1328 2.048033 TGCGGGCGTCGTACAATT 60.048 55.556 0.00 0.00 41.72 2.32
1326 1336 2.285602 GGCGTCGTACAATTACTGCATG 60.286 50.000 0.00 0.00 0.00 4.06
1328 1338 3.183754 CGTCGTACAATTACTGCATGGA 58.816 45.455 0.00 0.00 0.00 3.41
1336 1346 5.312895 ACAATTACTGCATGGACAAGTACA 58.687 37.500 0.00 0.00 0.00 2.90
1341 1351 4.905429 ACTGCATGGACAAGTACAACATA 58.095 39.130 0.00 0.00 0.00 2.29
1345 1355 4.094887 GCATGGACAAGTACAACATAGTGG 59.905 45.833 0.00 0.00 0.00 4.00
1346 1356 4.967084 TGGACAAGTACAACATAGTGGT 57.033 40.909 0.00 0.00 0.00 4.16
1350 1360 5.408604 GGACAAGTACAACATAGTGGTGAAG 59.591 44.000 1.43 0.00 37.20 3.02
1357 1367 6.114187 ACAACATAGTGGTGAAGAAGATCA 57.886 37.500 1.43 0.00 37.20 2.92
1358 1368 6.533730 ACAACATAGTGGTGAAGAAGATCAA 58.466 36.000 1.43 0.00 37.20 2.57
1410 1420 2.893489 GTTCCAAACCTTCAAGCAGGAT 59.107 45.455 0.00 0.00 37.39 3.24
1462 1472 0.038021 TGCTCATAACTTGCAGCCCA 59.962 50.000 0.00 0.00 31.45 5.36
1542 1552 3.182590 TTGCTCGCTGGCACTCCTT 62.183 57.895 0.00 0.00 42.27 3.36
1717 1981 2.627945 TCCATATGACGTTGCTTCCAC 58.372 47.619 3.65 0.00 0.00 4.02
1718 1982 1.327460 CCATATGACGTTGCTTCCACG 59.673 52.381 3.65 0.00 0.00 4.94
1719 1983 1.006832 ATATGACGTTGCTTCCACGC 58.993 50.000 0.00 0.00 0.00 5.34
1727 1991 1.861542 TTGCTTCCACGCAAATCCCG 61.862 55.000 0.00 0.00 46.00 5.14
1872 9776 2.035066 CAGTTGCAAAGTTCCTCCCAAG 59.965 50.000 0.00 0.00 0.00 3.61
1874 9778 1.981256 TGCAAAGTTCCTCCCAAGTC 58.019 50.000 0.00 0.00 0.00 3.01
1875 9779 1.214175 TGCAAAGTTCCTCCCAAGTCA 59.786 47.619 0.00 0.00 0.00 3.41
1882 9786 0.329261 TCCTCCCAAGTCAAGCCATG 59.671 55.000 0.00 0.00 0.00 3.66
1917 10792 3.256704 TCCTTTGGGTCCATGTCTAGTT 58.743 45.455 0.00 0.00 0.00 2.24
1941 10973 0.332632 CACCCATCTCCCACCATGTT 59.667 55.000 0.00 0.00 0.00 2.71
1950 10982 0.167251 CCCACCATGTTTACGAACGC 59.833 55.000 0.00 0.00 38.65 4.84
1979 11011 3.710722 CGCACTCTGGGCCTCCTT 61.711 66.667 4.53 0.00 0.00 3.36
1984 11016 3.011517 TCTGGGCCTCCTTGCTCC 61.012 66.667 4.53 0.00 0.00 4.70
1985 11017 4.479993 CTGGGCCTCCTTGCTCCG 62.480 72.222 4.53 0.00 0.00 4.63
2009 12688 3.614870 GCAATTTCAACCGCCAGATCTTT 60.615 43.478 0.00 0.00 0.00 2.52
2021 12700 4.878397 CGCCAGATCTTTCCTCAAACTAAT 59.122 41.667 0.00 0.00 0.00 1.73
2031 12710 7.770897 TCTTTCCTCAAACTAATCTAAGCCATC 59.229 37.037 0.00 0.00 0.00 3.51
2032 12711 6.560003 TCCTCAAACTAATCTAAGCCATCA 57.440 37.500 0.00 0.00 0.00 3.07
2044 12723 6.499106 TCTAAGCCATCATTTAGGATGTGA 57.501 37.500 3.99 0.00 42.47 3.58
2045 12724 6.899089 TCTAAGCCATCATTTAGGATGTGAA 58.101 36.000 3.99 0.00 42.47 3.18
2047 12726 4.210331 AGCCATCATTTAGGATGTGAACC 58.790 43.478 3.99 0.00 42.47 3.62
2050 12729 5.439721 CCATCATTTAGGATGTGAACCAGA 58.560 41.667 3.99 0.00 42.47 3.86
2063 12742 5.365619 TGTGAACCAGACTTCTTTCTTACC 58.634 41.667 0.00 0.00 0.00 2.85
2064 12743 5.130477 TGTGAACCAGACTTCTTTCTTACCT 59.870 40.000 0.00 0.00 0.00 3.08
2073 12752 6.763610 AGACTTCTTTCTTACCTTGAGTTGTG 59.236 38.462 0.00 0.00 0.00 3.33
2121 12800 2.766925 GCATGGTCCTGGCCCCATA 61.767 63.158 10.57 0.00 39.44 2.74
2135 12814 2.723273 CCCCATAACACAAGGACCTTC 58.277 52.381 2.91 0.00 0.00 3.46
2136 12815 2.041081 CCCCATAACACAAGGACCTTCA 59.959 50.000 2.91 0.00 0.00 3.02
2145 12824 3.733709 AGGACCTTCAGTGCTTTGG 57.266 52.632 0.00 0.00 46.50 3.28
2146 12825 0.846693 AGGACCTTCAGTGCTTTGGT 59.153 50.000 0.00 0.00 46.50 3.67
2148 12827 1.680338 GACCTTCAGTGCTTTGGTGT 58.320 50.000 0.00 0.00 0.00 4.16
2149 12828 1.334869 GACCTTCAGTGCTTTGGTGTG 59.665 52.381 0.00 0.00 0.00 3.82
2150 12829 0.670162 CCTTCAGTGCTTTGGTGTGG 59.330 55.000 0.00 0.00 0.00 4.17
2151 12830 1.392589 CTTCAGTGCTTTGGTGTGGT 58.607 50.000 0.00 0.00 0.00 4.16
2153 12832 0.034574 TCAGTGCTTTGGTGTGGTGT 60.035 50.000 0.00 0.00 0.00 4.16
2155 12834 0.034574 AGTGCTTTGGTGTGGTGTGA 60.035 50.000 0.00 0.00 0.00 3.58
2158 12837 1.383456 GCTTTGGTGTGGTGTGAGCA 61.383 55.000 0.00 0.00 0.00 4.26
2159 12838 1.102154 CTTTGGTGTGGTGTGAGCAA 58.898 50.000 0.00 0.00 0.00 3.91
2160 12839 1.476085 CTTTGGTGTGGTGTGAGCAAA 59.524 47.619 0.00 0.00 37.26 3.68
2161 12840 1.774110 TTGGTGTGGTGTGAGCAAAT 58.226 45.000 0.00 0.00 0.00 2.32
2162 12841 2.647683 TGGTGTGGTGTGAGCAAATA 57.352 45.000 0.00 0.00 0.00 1.40
2163 12842 3.153369 TGGTGTGGTGTGAGCAAATAT 57.847 42.857 0.00 0.00 0.00 1.28
2164 12843 3.081061 TGGTGTGGTGTGAGCAAATATC 58.919 45.455 0.00 0.00 0.00 1.63
2165 12844 3.244875 TGGTGTGGTGTGAGCAAATATCT 60.245 43.478 0.00 0.00 0.00 1.98
2166 12845 3.758554 GGTGTGGTGTGAGCAAATATCTT 59.241 43.478 0.00 0.00 0.00 2.40
2167 12846 4.218417 GGTGTGGTGTGAGCAAATATCTTT 59.782 41.667 0.00 0.00 0.00 2.52
2168 12847 5.278957 GGTGTGGTGTGAGCAAATATCTTTT 60.279 40.000 0.00 0.00 0.00 2.27
2169 12848 5.858581 GTGTGGTGTGAGCAAATATCTTTTC 59.141 40.000 0.00 0.00 0.00 2.29
2171 12850 5.000591 TGGTGTGAGCAAATATCTTTTCGA 58.999 37.500 0.00 0.00 0.00 3.71
2172 12851 5.471797 TGGTGTGAGCAAATATCTTTTCGAA 59.528 36.000 0.00 0.00 0.00 3.71
2173 12852 5.795441 GGTGTGAGCAAATATCTTTTCGAAC 59.205 40.000 0.00 0.00 0.00 3.95
2174 12853 6.370593 GTGTGAGCAAATATCTTTTCGAACA 58.629 36.000 0.00 0.00 0.00 3.18
2175 12854 6.303259 GTGTGAGCAAATATCTTTTCGAACAC 59.697 38.462 0.00 0.00 29.46 3.32
2176 12855 6.017523 TGTGAGCAAATATCTTTTCGAACACA 60.018 34.615 0.00 1.11 0.00 3.72
2177 12856 7.023575 GTGAGCAAATATCTTTTCGAACACAT 58.976 34.615 0.00 0.00 0.00 3.21
2178 12857 7.007725 GTGAGCAAATATCTTTTCGAACACATG 59.992 37.037 0.00 0.00 0.00 3.21
2180 12859 6.071952 AGCAAATATCTTTTCGAACACATGGT 60.072 34.615 0.00 0.00 0.00 3.55
2181 12860 6.033831 GCAAATATCTTTTCGAACACATGGTG 59.966 38.462 0.00 0.00 39.75 4.17
2183 12862 2.571212 TCTTTTCGAACACATGGTGCT 58.429 42.857 0.00 0.00 36.98 4.40
2185 12864 1.234821 TTTCGAACACATGGTGCTCC 58.765 50.000 0.00 0.00 36.98 4.70
2187 12866 1.003355 CGAACACATGGTGCTCCCT 60.003 57.895 1.59 0.00 36.98 4.20
2189 12868 1.003355 AACACATGGTGCTCCCTCG 60.003 57.895 1.59 0.00 36.98 4.63
2190 12869 1.480212 AACACATGGTGCTCCCTCGA 61.480 55.000 1.59 0.00 36.98 4.04
2191 12870 1.296392 CACATGGTGCTCCCTCGAA 59.704 57.895 1.59 0.00 0.00 3.71
2192 12871 1.021390 CACATGGTGCTCCCTCGAAC 61.021 60.000 1.59 0.00 0.00 3.95
2193 12872 1.450312 CATGGTGCTCCCTCGAACC 60.450 63.158 1.59 0.00 0.00 3.62
2194 12873 2.670148 ATGGTGCTCCCTCGAACCC 61.670 63.158 1.59 0.00 31.30 4.11
2195 12874 3.003763 GGTGCTCCCTCGAACCCT 61.004 66.667 0.00 0.00 0.00 4.34
2197 12876 1.375326 GTGCTCCCTCGAACCCTTT 59.625 57.895 0.00 0.00 0.00 3.11
2199 12878 1.125093 TGCTCCCTCGAACCCTTTGA 61.125 55.000 0.00 0.00 0.00 2.69
2200 12879 0.036306 GCTCCCTCGAACCCTTTGAA 59.964 55.000 0.00 0.00 0.00 2.69
2201 12880 1.809684 CTCCCTCGAACCCTTTGAAC 58.190 55.000 0.00 0.00 0.00 3.18
2202 12881 0.399075 TCCCTCGAACCCTTTGAACC 59.601 55.000 0.00 0.00 0.00 3.62
2203 12882 0.608308 CCCTCGAACCCTTTGAACCC 60.608 60.000 0.00 0.00 0.00 4.11
2204 12883 0.400594 CCTCGAACCCTTTGAACCCT 59.599 55.000 0.00 0.00 0.00 4.34
2205 12884 1.202891 CCTCGAACCCTTTGAACCCTT 60.203 52.381 0.00 0.00 0.00 3.95
2206 12885 2.583143 CTCGAACCCTTTGAACCCTTT 58.417 47.619 0.00 0.00 0.00 3.11
2207 12886 2.293399 CTCGAACCCTTTGAACCCTTTG 59.707 50.000 0.00 0.00 0.00 2.77
2208 12887 2.092321 TCGAACCCTTTGAACCCTTTGA 60.092 45.455 0.00 0.00 0.00 2.69
2209 12888 2.691011 CGAACCCTTTGAACCCTTTGAA 59.309 45.455 0.00 0.00 0.00 2.69
2211 12890 3.108847 ACCCTTTGAACCCTTTGAACA 57.891 42.857 0.00 0.00 0.00 3.18
2212 12891 2.764010 ACCCTTTGAACCCTTTGAACAC 59.236 45.455 0.00 0.00 0.00 3.32
2213 12892 2.102420 CCCTTTGAACCCTTTGAACACC 59.898 50.000 0.00 0.00 0.00 4.16
2215 12894 1.394618 TTGAACCCTTTGAACACCGG 58.605 50.000 0.00 0.00 0.00 5.28
2216 12895 1.104577 TGAACCCTTTGAACACCGGC 61.105 55.000 0.00 0.00 0.00 6.13
2217 12896 1.076632 AACCCTTTGAACACCGGCA 60.077 52.632 0.00 0.00 0.00 5.69
2218 12897 1.388837 AACCCTTTGAACACCGGCAC 61.389 55.000 0.00 0.00 0.00 5.01
2219 12898 2.561037 CCCTTTGAACACCGGCACC 61.561 63.158 0.00 0.00 0.00 5.01
2220 12899 2.561037 CCTTTGAACACCGGCACCC 61.561 63.158 0.00 0.00 0.00 4.61
2221 12900 2.519780 TTTGAACACCGGCACCCC 60.520 61.111 0.00 0.00 0.00 4.95
2222 12901 3.360423 TTTGAACACCGGCACCCCA 62.360 57.895 0.00 0.00 0.00 4.96
2223 12902 3.783362 TTGAACACCGGCACCCCAG 62.783 63.158 0.00 0.00 0.00 4.45
2233 12912 4.778143 CACCCCAGCGGCCTACAC 62.778 72.222 0.00 0.00 33.26 2.90
2235 12914 4.473520 CCCCAGCGGCCTACACAG 62.474 72.222 0.00 0.00 0.00 3.66
2272 12951 4.514577 AGACCCGAGCGGCGAATG 62.515 66.667 12.98 0.00 44.57 2.67
2276 12955 4.520846 CCGAGCGGCGAATGCAAC 62.521 66.667 12.98 0.00 45.35 4.17
2277 12956 3.787676 CGAGCGGCGAATGCAACA 61.788 61.111 12.98 0.00 45.35 3.33
2278 12957 2.202349 GAGCGGCGAATGCAACAC 60.202 61.111 12.98 0.00 45.35 3.32
2279 12958 3.667429 GAGCGGCGAATGCAACACC 62.667 63.158 12.98 0.00 45.35 4.16
2281 12960 3.722295 CGGCGAATGCAACACCGT 61.722 61.111 0.00 0.00 45.35 4.83
2282 12961 2.126888 GGCGAATGCAACACCGTG 60.127 61.111 0.00 0.00 45.35 4.94
2283 12962 2.800746 GCGAATGCAACACCGTGC 60.801 61.111 0.00 0.00 45.15 5.34
2299 12978 4.626081 GCGGAGGCGGCCATACAT 62.626 66.667 23.09 0.00 0.00 2.29
2300 12979 3.056458 CGGAGGCGGCCATACATA 58.944 61.111 23.09 0.00 0.00 2.29
2301 12980 1.374252 CGGAGGCGGCCATACATAC 60.374 63.158 23.09 0.00 0.00 2.39
2302 12981 1.374252 GGAGGCGGCCATACATACG 60.374 63.158 23.09 0.00 0.00 3.06
2305 12984 3.411351 GCGGCCATACATACGCGG 61.411 66.667 12.47 0.00 42.66 6.46
2306 12985 3.411351 CGGCCATACATACGCGGC 61.411 66.667 12.47 0.13 44.10 6.53
2308 12987 3.411351 GCCATACATACGCGGCGG 61.411 66.667 27.37 11.48 34.26 6.13
2310 12989 1.733041 CCATACATACGCGGCGGAG 60.733 63.158 27.37 17.26 0.00 4.63
2311 12990 1.284715 CATACATACGCGGCGGAGA 59.715 57.895 27.37 11.80 0.00 3.71
2312 12991 1.002250 CATACATACGCGGCGGAGAC 61.002 60.000 27.37 0.00 0.00 3.36
2324 13003 3.221222 GGAGACGGGAGGTGATGG 58.779 66.667 0.00 0.00 0.00 3.51
2325 13004 1.381327 GGAGACGGGAGGTGATGGA 60.381 63.158 0.00 0.00 0.00 3.41
2328 13007 2.284625 ACGGGAGGTGATGGAGCA 60.285 61.111 0.00 0.00 0.00 4.26
2330 13009 2.362369 CGGGAGGTGATGGAGCAGT 61.362 63.158 0.00 0.00 0.00 4.40
2331 13010 1.524482 GGGAGGTGATGGAGCAGTC 59.476 63.158 0.00 0.00 0.00 3.51
2332 13011 1.524482 GGAGGTGATGGAGCAGTCC 59.476 63.158 0.00 0.00 44.24 3.85
2333 13012 1.524482 GAGGTGATGGAGCAGTCCC 59.476 63.158 0.00 0.00 43.15 4.46
2334 13013 1.229625 AGGTGATGGAGCAGTCCCA 60.230 57.895 0.00 0.00 43.15 4.37
2335 13014 0.622738 AGGTGATGGAGCAGTCCCAT 60.623 55.000 0.00 0.00 46.40 4.00
2336 13015 0.257039 GGTGATGGAGCAGTCCCATT 59.743 55.000 0.00 0.00 43.96 3.16
2337 13016 1.341383 GGTGATGGAGCAGTCCCATTT 60.341 52.381 0.00 0.00 43.96 2.32
2339 13018 1.341285 TGATGGAGCAGTCCCATTTGG 60.341 52.381 0.00 0.00 43.96 3.28
2340 13019 1.002069 ATGGAGCAGTCCCATTTGGA 58.998 50.000 0.00 0.00 41.36 3.53
2341 13020 0.329261 TGGAGCAGTCCCATTTGGAG 59.671 55.000 0.00 0.00 46.38 3.86
2342 13021 1.034292 GGAGCAGTCCCATTTGGAGC 61.034 60.000 0.00 0.00 46.38 4.70
2343 13022 0.322816 GAGCAGTCCCATTTGGAGCA 60.323 55.000 0.00 0.00 46.38 4.26
2344 13023 0.323178 AGCAGTCCCATTTGGAGCAG 60.323 55.000 0.00 0.00 46.38 4.24
2345 13024 1.318158 GCAGTCCCATTTGGAGCAGG 61.318 60.000 0.00 0.00 46.38 4.85
2347 13026 2.054453 GTCCCATTTGGAGCAGGGC 61.054 63.158 0.00 0.00 46.38 5.19
2348 13027 2.761213 CCCATTTGGAGCAGGGCC 60.761 66.667 0.00 0.00 37.39 5.80
2349 13028 3.142838 CCATTTGGAGCAGGGCCG 61.143 66.667 0.00 0.00 37.39 6.13
2350 13029 3.830192 CATTTGGAGCAGGGCCGC 61.830 66.667 11.60 11.60 0.00 6.53
2394 13073 4.543736 GCAGACGCGCGAACGATG 62.544 66.667 39.36 24.98 43.93 3.84
2395 13074 3.902063 CAGACGCGCGAACGATGG 61.902 66.667 39.36 13.98 43.93 3.51
2443 13122 4.214327 GCTCGGCCGAAGAGGAGG 62.214 72.222 30.53 16.60 45.00 4.30
2450 13129 2.885861 CGAAGAGGAGGTCGGGTG 59.114 66.667 0.00 0.00 33.62 4.61
2451 13130 2.711922 CGAAGAGGAGGTCGGGTGG 61.712 68.421 0.00 0.00 33.62 4.61
2453 13132 1.605971 GAAGAGGAGGTCGGGTGGTC 61.606 65.000 0.00 0.00 0.00 4.02
2467 13146 4.409218 GGTCGCGCCAGTGTCGTA 62.409 66.667 13.61 0.00 37.17 3.43
2468 13147 2.874780 GTCGCGCCAGTGTCGTAG 60.875 66.667 0.00 0.00 0.00 3.51
2470 13149 2.034317 TCGCGCCAGTGTCGTAGTA 61.034 57.895 0.00 0.00 0.00 1.82
2472 13151 1.798735 GCGCCAGTGTCGTAGTAGA 59.201 57.895 0.00 0.00 0.00 2.59
2473 13152 0.248134 GCGCCAGTGTCGTAGTAGAG 60.248 60.000 0.00 0.00 0.00 2.43
2474 13153 0.377554 CGCCAGTGTCGTAGTAGAGG 59.622 60.000 0.00 0.00 0.00 3.69
2475 13154 0.100861 GCCAGTGTCGTAGTAGAGGC 59.899 60.000 0.00 0.00 0.00 4.70
2477 13156 1.132643 CCAGTGTCGTAGTAGAGGCAC 59.867 57.143 2.92 2.92 0.00 5.01
2478 13157 1.085091 AGTGTCGTAGTAGAGGCACG 58.915 55.000 5.09 0.00 37.03 5.34
2479 13158 0.522915 GTGTCGTAGTAGAGGCACGC 60.523 60.000 0.00 0.00 35.70 5.34
2480 13159 1.297451 GTCGTAGTAGAGGCACGCG 60.297 63.158 3.53 3.53 35.70 6.01
2481 13160 2.024305 CGTAGTAGAGGCACGCGG 59.976 66.667 12.47 0.00 0.00 6.46
2482 13161 2.412112 GTAGTAGAGGCACGCGGG 59.588 66.667 12.47 7.92 0.00 6.13
2483 13162 2.831742 TAGTAGAGGCACGCGGGG 60.832 66.667 11.92 2.33 0.00 5.73
2511 13190 4.090057 GCTGCGGGCGACTCAAAC 62.090 66.667 0.00 0.00 0.00 2.93
2512 13191 3.423154 CTGCGGGCGACTCAAACC 61.423 66.667 0.00 0.00 0.00 3.27
2517 13196 3.110178 GGCGACTCAAACCGACCG 61.110 66.667 0.00 0.00 0.00 4.79
2519 13198 1.081242 GCGACTCAAACCGACCGTA 60.081 57.895 0.00 0.00 0.00 4.02
2520 13199 1.069378 GCGACTCAAACCGACCGTAG 61.069 60.000 0.00 0.00 0.00 3.51
2521 13200 0.518636 CGACTCAAACCGACCGTAGA 59.481 55.000 0.00 0.00 0.00 2.59
2522 13201 1.131883 CGACTCAAACCGACCGTAGAT 59.868 52.381 0.00 0.00 0.00 1.98
2523 13202 2.790468 CGACTCAAACCGACCGTAGATC 60.790 54.545 0.00 0.00 0.00 2.75
2526 13205 2.019249 TCAAACCGACCGTAGATCGAT 58.981 47.619 0.00 0.00 42.86 3.59
2527 13206 3.205338 TCAAACCGACCGTAGATCGATA 58.795 45.455 0.00 0.00 42.86 2.92
2528 13207 3.627123 TCAAACCGACCGTAGATCGATAA 59.373 43.478 0.00 0.00 42.86 1.75
2530 13209 3.615849 ACCGACCGTAGATCGATAAAC 57.384 47.619 0.00 0.00 42.86 2.01
2531 13210 2.291741 ACCGACCGTAGATCGATAAACC 59.708 50.000 0.00 0.00 42.86 3.27
2533 13212 3.243168 CCGACCGTAGATCGATAAACCAA 60.243 47.826 0.00 0.00 42.86 3.67
2534 13213 4.353737 CGACCGTAGATCGATAAACCAAA 58.646 43.478 0.00 0.00 42.86 3.28
2535 13214 4.799949 CGACCGTAGATCGATAAACCAAAA 59.200 41.667 0.00 0.00 42.86 2.44
2536 13215 5.289193 CGACCGTAGATCGATAAACCAAAAA 59.711 40.000 0.00 0.00 42.86 1.94
2537 13216 6.507456 CGACCGTAGATCGATAAACCAAAAAG 60.507 42.308 0.00 0.00 42.86 2.27
2538 13217 6.400568 ACCGTAGATCGATAAACCAAAAAGA 58.599 36.000 0.00 0.00 42.86 2.52
2540 13219 7.388500 ACCGTAGATCGATAAACCAAAAAGAAA 59.612 33.333 0.00 0.00 42.86 2.52
2542 13221 9.601971 CGTAGATCGATAAACCAAAAAGAAAAA 57.398 29.630 0.00 0.00 42.86 1.94
2544 13223 8.502161 AGATCGATAAACCAAAAAGAAAAACG 57.498 30.769 0.00 0.00 0.00 3.60
2545 13224 6.499356 TCGATAAACCAAAAAGAAAAACGC 57.501 33.333 0.00 0.00 0.00 4.84
2546 13225 5.459434 TCGATAAACCAAAAAGAAAAACGCC 59.541 36.000 0.00 0.00 0.00 5.68
2547 13226 5.608630 CGATAAACCAAAAAGAAAAACGCCG 60.609 40.000 0.00 0.00 0.00 6.46
2548 13227 2.943449 ACCAAAAAGAAAAACGCCGA 57.057 40.000 0.00 0.00 0.00 5.54
2550 13229 3.377439 ACCAAAAAGAAAAACGCCGATC 58.623 40.909 0.00 0.00 0.00 3.69
2551 13230 3.181485 ACCAAAAAGAAAAACGCCGATCA 60.181 39.130 0.00 0.00 0.00 2.92
2552 13231 3.799420 CCAAAAAGAAAAACGCCGATCAA 59.201 39.130 0.00 0.00 0.00 2.57
2553 13232 4.085107 CCAAAAAGAAAAACGCCGATCAAG 60.085 41.667 0.00 0.00 0.00 3.02
2554 13233 4.561735 AAAAGAAAAACGCCGATCAAGA 57.438 36.364 0.00 0.00 0.00 3.02
2556 13235 1.459592 AGAAAAACGCCGATCAAGACG 59.540 47.619 0.00 0.00 0.00 4.18
2557 13236 1.458064 GAAAAACGCCGATCAAGACGA 59.542 47.619 0.00 0.00 0.00 4.20
2558 13237 0.788391 AAAACGCCGATCAAGACGAC 59.212 50.000 0.00 0.00 0.00 4.34
2559 13238 1.012486 AAACGCCGATCAAGACGACC 61.012 55.000 0.00 0.00 0.00 4.79
2561 13240 2.582498 GCCGATCAAGACGACCGG 60.582 66.667 0.00 0.00 42.74 5.28
2564 13243 2.488355 GATCAAGACGACCGGCGA 59.512 61.111 22.10 2.72 44.57 5.54
2565 13244 1.586564 GATCAAGACGACCGGCGAG 60.587 63.158 22.10 7.51 44.57 5.03
2566 13245 1.989966 GATCAAGACGACCGGCGAGA 61.990 60.000 22.10 14.33 44.57 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.054799 TGTCAAGTAGCCTCCCAAAGT 58.945 47.619 0.00 0.00 0.00 2.66
15 16 3.073798 TCAAAATGTCAAGTAGCCTCCCA 59.926 43.478 0.00 0.00 0.00 4.37
118 119 4.832608 GCGCGACCGAGGGGAAAT 62.833 66.667 12.10 0.00 36.97 2.17
176 179 1.154430 TGAGGTTAACCCAAAGCCCT 58.846 50.000 21.30 0.00 36.42 5.19
190 193 1.073923 CCCAAACTACAGCCTTGAGGT 59.926 52.381 0.00 0.00 37.57 3.85
226 229 0.843309 ATCATATGTTGGGTCGGCCA 59.157 50.000 9.07 0.00 36.17 5.36
268 271 3.252215 CAGCCGTGTTATTCTTGTTTCCA 59.748 43.478 0.00 0.00 0.00 3.53
382 385 1.997874 GGCAGTGACTCCCCCATCT 60.998 63.158 0.00 0.00 0.00 2.90
399 402 2.827921 CCCCTTCTCCTTTGACAATTGG 59.172 50.000 10.83 0.00 0.00 3.16
464 467 9.562583 GTGAAGCGACAAAAACCATATTATAAA 57.437 29.630 0.00 0.00 0.00 1.40
465 468 8.185505 GGTGAAGCGACAAAAACCATATTATAA 58.814 33.333 0.00 0.00 0.00 0.98
466 469 7.337184 TGGTGAAGCGACAAAAACCATATTATA 59.663 33.333 0.00 0.00 32.88 0.98
475 478 6.580476 CATTTATTGGTGAAGCGACAAAAAC 58.420 36.000 0.00 0.00 0.00 2.43
773 782 9.645059 ATGTGATGTATATCCGATACAGAAAAG 57.355 33.333 3.98 0.00 37.84 2.27
892 902 3.230134 TGCTGCCAAGAACCAATAAAGT 58.770 40.909 0.00 0.00 0.00 2.66
897 907 1.074405 TCTCTGCTGCCAAGAACCAAT 59.926 47.619 0.00 0.00 0.00 3.16
909 919 6.037610 ACGGCTTTTATAGAATTTCTCTGCTG 59.962 38.462 1.27 7.18 35.41 4.41
985 995 4.494855 GCTCTTCATTATCGTTTCCTGTGC 60.495 45.833 0.00 0.00 0.00 4.57
995 1005 3.496130 GGTGGTCATGCTCTTCATTATCG 59.504 47.826 0.00 0.00 31.79 2.92
998 1008 3.609853 GTGGTGGTCATGCTCTTCATTA 58.390 45.455 0.00 0.00 31.79 1.90
1012 1022 1.833187 AGGGCATATATGGTGGTGGT 58.167 50.000 14.51 0.00 0.00 4.16
1038 1048 1.742308 AGGTGGTGGTGGTTAGTGAT 58.258 50.000 0.00 0.00 0.00 3.06
1191 1201 2.099831 GCGTACTCGGTGACCTCG 59.900 66.667 0.00 0.00 37.56 4.63
1263 1273 6.459573 GCGATGGGTTCTGCAATAAATTCTTA 60.460 38.462 0.00 0.00 0.00 2.10
1272 1282 0.749454 GGAGCGATGGGTTCTGCAAT 60.749 55.000 0.00 0.00 0.00 3.56
1308 1318 3.930229 TGTCCATGCAGTAATTGTACGAC 59.070 43.478 0.00 0.00 35.20 4.34
1309 1319 4.195225 TGTCCATGCAGTAATTGTACGA 57.805 40.909 0.00 0.00 35.20 3.43
1315 1325 5.767665 TGTTGTACTTGTCCATGCAGTAATT 59.232 36.000 0.00 0.00 0.00 1.40
1318 1328 4.344359 TGTTGTACTTGTCCATGCAGTA 57.656 40.909 0.00 0.00 0.00 2.74
1326 1336 4.890088 TCACCACTATGTTGTACTTGTCC 58.110 43.478 0.00 0.00 0.00 4.02
1328 1338 6.169557 TCTTCACCACTATGTTGTACTTGT 57.830 37.500 0.00 0.00 0.00 3.16
1336 1346 6.150140 GCTTTGATCTTCTTCACCACTATGTT 59.850 38.462 0.00 0.00 0.00 2.71
1341 1351 3.181440 TGGCTTTGATCTTCTTCACCACT 60.181 43.478 0.00 0.00 0.00 4.00
1345 1355 3.935203 TCGATGGCTTTGATCTTCTTCAC 59.065 43.478 0.00 0.00 0.00 3.18
1346 1356 4.206477 TCGATGGCTTTGATCTTCTTCA 57.794 40.909 0.00 0.00 0.00 3.02
1350 1360 5.388944 GCATTATCGATGGCTTTGATCTTC 58.611 41.667 8.54 0.00 36.21 2.87
1410 1420 0.592637 CAGCGACAACATCCTTGCAA 59.407 50.000 0.00 0.00 0.00 4.08
1424 1434 1.998285 CAATCGTCGATTGCAGCGA 59.002 52.632 29.30 9.32 41.99 4.93
1468 1478 3.334691 TCTTGTACAAAGGCGAAGATGG 58.665 45.455 10.03 0.00 0.00 3.51
1542 1552 0.323302 TCCATTGCTTAGCGACACCA 59.677 50.000 0.00 0.00 0.00 4.17
1650 1691 8.102047 TCAAATCTATTGGTGCCAATGAAATTT 58.898 29.630 22.67 19.56 45.15 1.82
1718 1982 1.356624 CCTTGATCGCGGGATTTGC 59.643 57.895 16.82 4.61 31.51 3.68
1719 1983 1.447317 CCCCTTGATCGCGGGATTTG 61.447 60.000 16.82 9.38 43.44 2.32
1723 1987 1.052124 AATACCCCTTGATCGCGGGA 61.052 55.000 18.17 4.03 43.44 5.14
1727 1991 3.805207 AGTTGTAATACCCCTTGATCGC 58.195 45.455 0.00 0.00 0.00 4.58
1872 9776 2.489938 TGGAACCTACATGGCTTGAC 57.510 50.000 7.45 0.00 40.22 3.18
1874 9778 2.689983 GGAATGGAACCTACATGGCTTG 59.310 50.000 0.00 0.00 40.22 4.01
1875 9779 2.582636 AGGAATGGAACCTACATGGCTT 59.417 45.455 0.00 0.00 40.22 4.35
1882 9786 3.621558 CCAAAGGAGGAATGGAACCTAC 58.378 50.000 0.00 0.00 37.93 3.18
1917 10792 0.918983 GGTGGGAGATGGGTGATCAA 59.081 55.000 0.00 0.00 32.86 2.57
1963 10995 2.045536 CAAGGAGGCCCAGAGTGC 60.046 66.667 0.00 0.00 33.88 4.40
1967 10999 3.011517 GGAGCAAGGAGGCCCAGA 61.012 66.667 0.00 0.00 33.88 3.86
1984 11016 2.126110 GGCGGTTGAAATTGCCCG 60.126 61.111 0.00 0.00 41.70 6.13
2009 12688 6.560003 TGATGGCTTAGATTAGTTTGAGGA 57.440 37.500 0.00 0.00 0.00 3.71
2021 12700 6.499106 TCACATCCTAAATGATGGCTTAGA 57.501 37.500 6.04 0.00 45.16 2.10
2031 12710 6.176183 AGAAGTCTGGTTCACATCCTAAATG 58.824 40.000 0.00 0.00 0.00 2.32
2032 12711 6.380079 AGAAGTCTGGTTCACATCCTAAAT 57.620 37.500 0.00 0.00 0.00 1.40
2044 12723 6.126739 ACTCAAGGTAAGAAAGAAGTCTGGTT 60.127 38.462 0.00 0.00 0.00 3.67
2045 12724 5.367060 ACTCAAGGTAAGAAAGAAGTCTGGT 59.633 40.000 0.00 0.00 0.00 4.00
2047 12726 6.763610 ACAACTCAAGGTAAGAAAGAAGTCTG 59.236 38.462 0.00 0.00 0.00 3.51
2050 12729 6.415573 ACACAACTCAAGGTAAGAAAGAAGT 58.584 36.000 0.00 0.00 0.00 3.01
2063 12742 3.248363 TCGCATGAGAAACACAACTCAAG 59.752 43.478 0.00 0.00 44.47 3.02
2064 12743 3.002246 GTCGCATGAGAAACACAACTCAA 59.998 43.478 0.00 0.00 44.47 3.02
2073 12752 0.445436 CTGGCAGTCGCATGAGAAAC 59.555 55.000 6.28 0.00 41.24 2.78
2101 12780 4.512914 GGGGCCAGGACCATGCTC 62.513 72.222 15.62 0.00 27.52 4.26
2121 12800 1.212935 AGCACTGAAGGTCCTTGTGTT 59.787 47.619 18.55 12.63 0.00 3.32
2135 12814 0.101040 CACACCACACCAAAGCACTG 59.899 55.000 0.00 0.00 0.00 3.66
2136 12815 0.034574 TCACACCACACCAAAGCACT 60.035 50.000 0.00 0.00 0.00 4.40
2141 12820 1.550327 TTTGCTCACACCACACCAAA 58.450 45.000 0.00 0.00 0.00 3.28
2143 12822 2.647683 TATTTGCTCACACCACACCA 57.352 45.000 0.00 0.00 0.00 4.17
2145 12824 5.376854 AAAGATATTTGCTCACACCACAC 57.623 39.130 0.00 0.00 0.00 3.82
2146 12825 5.334802 CGAAAAGATATTTGCTCACACCACA 60.335 40.000 0.00 0.00 0.00 4.17
2148 12827 5.000591 TCGAAAAGATATTTGCTCACACCA 58.999 37.500 0.00 0.00 0.00 4.17
2149 12828 5.545658 TCGAAAAGATATTTGCTCACACC 57.454 39.130 0.00 0.00 0.00 4.16
2150 12829 6.303259 GTGTTCGAAAAGATATTTGCTCACAC 59.697 38.462 0.00 6.61 0.00 3.82
2151 12830 6.017523 TGTGTTCGAAAAGATATTTGCTCACA 60.018 34.615 0.00 2.24 31.39 3.58
2153 12832 6.552859 TGTGTTCGAAAAGATATTTGCTCA 57.447 33.333 0.00 0.00 0.00 4.26
2155 12834 6.071952 ACCATGTGTTCGAAAAGATATTTGCT 60.072 34.615 0.00 0.00 0.00 3.91
2158 12837 6.071952 AGCACCATGTGTTCGAAAAGATATTT 60.072 34.615 0.00 0.00 35.75 1.40
2159 12838 5.415701 AGCACCATGTGTTCGAAAAGATATT 59.584 36.000 0.00 0.00 35.75 1.28
2160 12839 4.943705 AGCACCATGTGTTCGAAAAGATAT 59.056 37.500 0.00 0.00 35.75 1.63
2161 12840 4.323417 AGCACCATGTGTTCGAAAAGATA 58.677 39.130 0.00 0.00 35.75 1.98
2162 12841 3.149196 AGCACCATGTGTTCGAAAAGAT 58.851 40.909 0.00 0.00 35.75 2.40
2163 12842 2.548057 GAGCACCATGTGTTCGAAAAGA 59.452 45.455 0.00 0.00 34.48 2.52
2164 12843 2.350772 GGAGCACCATGTGTTCGAAAAG 60.351 50.000 0.00 0.00 43.07 2.27
2165 12844 1.606668 GGAGCACCATGTGTTCGAAAA 59.393 47.619 0.00 0.00 43.07 2.29
2166 12845 1.234821 GGAGCACCATGTGTTCGAAA 58.765 50.000 0.00 0.00 43.07 3.46
2167 12846 0.605319 GGGAGCACCATGTGTTCGAA 60.605 55.000 1.58 0.00 43.07 3.71
2168 12847 1.003839 GGGAGCACCATGTGTTCGA 60.004 57.895 1.58 0.00 43.07 3.71
2169 12848 1.003355 AGGGAGCACCATGTGTTCG 60.003 57.895 1.58 0.00 43.07 3.95
2171 12850 1.003355 CGAGGGAGCACCATGTGTT 60.003 57.895 1.58 0.00 43.89 3.32
2172 12851 1.480212 TTCGAGGGAGCACCATGTGT 61.480 55.000 1.58 0.00 43.89 3.72
2173 12852 1.021390 GTTCGAGGGAGCACCATGTG 61.021 60.000 1.58 0.00 43.89 3.21
2174 12853 1.296715 GTTCGAGGGAGCACCATGT 59.703 57.895 1.58 0.00 43.89 3.21
2175 12854 1.450312 GGTTCGAGGGAGCACCATG 60.450 63.158 1.58 0.00 43.89 3.66
2176 12855 2.670148 GGGTTCGAGGGAGCACCAT 61.670 63.158 1.58 0.00 43.89 3.55
2177 12856 3.319198 GGGTTCGAGGGAGCACCA 61.319 66.667 1.58 0.00 43.89 4.17
2178 12857 2.125766 AAAGGGTTCGAGGGAGCACC 62.126 60.000 0.00 0.00 40.67 5.01
2180 12859 1.125093 TCAAAGGGTTCGAGGGAGCA 61.125 55.000 0.00 0.00 0.00 4.26
2181 12860 0.036306 TTCAAAGGGTTCGAGGGAGC 59.964 55.000 0.00 0.00 0.00 4.70
2183 12862 0.399075 GGTTCAAAGGGTTCGAGGGA 59.601 55.000 0.00 0.00 0.00 4.20
2185 12864 0.400594 AGGGTTCAAAGGGTTCGAGG 59.599 55.000 0.00 0.00 0.00 4.63
2187 12866 2.092321 TCAAAGGGTTCAAAGGGTTCGA 60.092 45.455 0.00 0.00 0.00 3.71
2189 12868 3.449377 TGTTCAAAGGGTTCAAAGGGTTC 59.551 43.478 0.00 0.00 0.00 3.62
2190 12869 3.196901 GTGTTCAAAGGGTTCAAAGGGTT 59.803 43.478 0.00 0.00 0.00 4.11
2191 12870 2.764010 GTGTTCAAAGGGTTCAAAGGGT 59.236 45.455 0.00 0.00 0.00 4.34
2192 12871 2.102420 GGTGTTCAAAGGGTTCAAAGGG 59.898 50.000 0.00 0.00 0.00 3.95
2193 12872 2.223711 CGGTGTTCAAAGGGTTCAAAGG 60.224 50.000 0.00 0.00 0.00 3.11
2194 12873 2.223711 CCGGTGTTCAAAGGGTTCAAAG 60.224 50.000 0.00 0.00 0.00 2.77
2195 12874 1.751924 CCGGTGTTCAAAGGGTTCAAA 59.248 47.619 0.00 0.00 0.00 2.69
2197 12876 1.104577 GCCGGTGTTCAAAGGGTTCA 61.105 55.000 1.90 0.00 0.00 3.18
2199 12878 1.076632 TGCCGGTGTTCAAAGGGTT 60.077 52.632 1.90 0.00 0.00 4.11
2200 12879 1.826487 GTGCCGGTGTTCAAAGGGT 60.826 57.895 1.90 0.00 0.00 4.34
2201 12880 2.561037 GGTGCCGGTGTTCAAAGGG 61.561 63.158 1.90 0.00 0.00 3.95
2202 12881 2.561037 GGGTGCCGGTGTTCAAAGG 61.561 63.158 1.90 0.00 0.00 3.11
2203 12882 2.561037 GGGGTGCCGGTGTTCAAAG 61.561 63.158 1.90 0.00 0.00 2.77
2204 12883 2.519780 GGGGTGCCGGTGTTCAAA 60.520 61.111 1.90 0.00 0.00 2.69
2205 12884 3.783362 CTGGGGTGCCGGTGTTCAA 62.783 63.158 1.90 0.00 0.00 2.69
2206 12885 4.263572 CTGGGGTGCCGGTGTTCA 62.264 66.667 1.90 0.00 0.00 3.18
2216 12895 4.778143 GTGTAGGCCGCTGGGGTG 62.778 72.222 12.70 0.00 38.44 4.61
2218 12897 4.473520 CTGTGTAGGCCGCTGGGG 62.474 72.222 6.36 6.36 39.58 4.96
2244 12923 4.530857 CGGGTCTGGCCGCTTAGG 62.531 72.222 0.00 0.00 44.97 2.69
2245 12924 3.432051 CTCGGGTCTGGCCGCTTAG 62.432 68.421 0.00 0.00 38.44 2.18
2254 12933 4.514577 ATTCGCCGCTCGGGTCTG 62.515 66.667 10.57 0.00 39.05 3.51
2255 12934 4.514577 CATTCGCCGCTCGGGTCT 62.515 66.667 10.57 0.00 39.05 3.85
2260 12939 3.787676 TGTTGCATTCGCCGCTCG 61.788 61.111 0.00 0.00 37.32 5.03
2261 12940 2.202349 GTGTTGCATTCGCCGCTC 60.202 61.111 0.00 0.00 37.32 5.03
2262 12941 3.737172 GGTGTTGCATTCGCCGCT 61.737 61.111 6.31 0.00 37.32 5.52
2265 12944 2.126888 CACGGTGTTGCATTCGCC 60.127 61.111 10.70 10.70 37.32 5.54
2267 12946 2.499520 CGCACGGTGTTGCATTCG 60.500 61.111 10.24 0.00 43.15 3.34
2268 12947 2.126888 CCGCACGGTGTTGCATTC 60.127 61.111 10.24 0.00 43.15 2.67
2269 12948 2.593148 TCCGCACGGTGTTGCATT 60.593 55.556 10.24 0.00 43.15 3.56
2270 12949 3.049674 CTCCGCACGGTGTTGCAT 61.050 61.111 10.24 0.00 43.15 3.96
2282 12961 3.234630 TATGTATGGCCGCCTCCGC 62.235 63.158 11.61 0.00 0.00 5.54
2283 12962 1.374252 GTATGTATGGCCGCCTCCG 60.374 63.158 11.61 0.00 0.00 4.63
2284 12963 1.374252 CGTATGTATGGCCGCCTCC 60.374 63.158 11.61 0.00 0.00 4.30
2287 12966 3.411351 CGCGTATGTATGGCCGCC 61.411 66.667 1.04 1.04 42.99 6.13
2288 12967 3.411351 CCGCGTATGTATGGCCGC 61.411 66.667 4.92 0.00 42.53 6.53
2289 12968 3.411351 GCCGCGTATGTATGGCCG 61.411 66.667 4.92 0.00 41.70 6.13
2290 12969 3.411351 CGCCGCGTATGTATGGCC 61.411 66.667 4.92 0.00 44.71 5.36
2291 12970 3.411351 CCGCCGCGTATGTATGGC 61.411 66.667 12.58 0.00 44.09 4.40
2292 12971 1.733041 CTCCGCCGCGTATGTATGG 60.733 63.158 12.58 0.00 0.00 2.74
2293 12972 1.002250 GTCTCCGCCGCGTATGTATG 61.002 60.000 12.58 0.00 0.00 2.39
2296 12975 4.547905 CGTCTCCGCCGCGTATGT 62.548 66.667 12.58 0.00 0.00 2.29
2305 12984 3.148279 ATCACCTCCCGTCTCCGC 61.148 66.667 0.00 0.00 0.00 5.54
2306 12985 2.786495 CCATCACCTCCCGTCTCCG 61.786 68.421 0.00 0.00 0.00 4.63
2308 12987 2.022240 GCTCCATCACCTCCCGTCTC 62.022 65.000 0.00 0.00 0.00 3.36
2310 12989 2.303549 CTGCTCCATCACCTCCCGTC 62.304 65.000 0.00 0.00 0.00 4.79
2311 12990 2.284625 TGCTCCATCACCTCCCGT 60.285 61.111 0.00 0.00 0.00 5.28
2312 12991 2.303549 GACTGCTCCATCACCTCCCG 62.304 65.000 0.00 0.00 0.00 5.14
2313 12992 1.524482 GACTGCTCCATCACCTCCC 59.476 63.158 0.00 0.00 0.00 4.30
2314 12993 1.524482 GGACTGCTCCATCACCTCC 59.476 63.158 0.00 0.00 36.42 4.30
2315 12994 1.267574 TGGGACTGCTCCATCACCTC 61.268 60.000 0.00 0.00 38.52 3.85
2316 12995 0.622738 ATGGGACTGCTCCATCACCT 60.623 55.000 0.00 0.00 40.74 4.00
2318 12997 1.747355 CAAATGGGACTGCTCCATCAC 59.253 52.381 3.36 0.00 43.61 3.06
2319 12998 1.341285 CCAAATGGGACTGCTCCATCA 60.341 52.381 3.36 0.00 43.61 3.07
2320 12999 1.064463 TCCAAATGGGACTGCTCCATC 60.064 52.381 0.00 0.00 43.61 3.51
2323 13002 1.034292 GCTCCAAATGGGACTGCTCC 61.034 60.000 0.00 0.00 42.15 4.70
2324 13003 0.322816 TGCTCCAAATGGGACTGCTC 60.323 55.000 0.00 0.00 42.15 4.26
2325 13004 0.323178 CTGCTCCAAATGGGACTGCT 60.323 55.000 0.00 0.00 42.15 4.24
2328 13007 1.693640 CCCTGCTCCAAATGGGACT 59.306 57.895 0.00 0.00 42.15 3.85
2330 13009 2.360191 GCCCTGCTCCAAATGGGA 59.640 61.111 0.00 0.00 45.89 4.37
2331 13010 2.761213 GGCCCTGCTCCAAATGGG 60.761 66.667 0.00 0.00 42.41 4.00
2332 13011 3.142838 CGGCCCTGCTCCAAATGG 61.143 66.667 0.00 0.00 0.00 3.16
2333 13012 3.830192 GCGGCCCTGCTCCAAATG 61.830 66.667 0.00 0.00 0.00 2.32
2349 13028 2.876645 CTCTTCGCCTGTCGTCGC 60.877 66.667 0.00 0.00 39.67 5.19
2350 13029 2.876645 GCTCTTCGCCTGTCGTCG 60.877 66.667 0.00 0.00 39.67 5.12
2351 13030 2.876645 CGCTCTTCGCCTGTCGTC 60.877 66.667 0.00 0.00 39.67 4.20
2352 13031 3.362797 TCGCTCTTCGCCTGTCGT 61.363 61.111 0.00 0.00 39.67 4.34
2353 13032 2.876645 GTCGCTCTTCGCCTGTCG 60.877 66.667 0.00 0.00 38.27 4.35
2354 13033 2.876645 CGTCGCTCTTCGCCTGTC 60.877 66.667 0.00 0.00 38.27 3.51
2355 13034 4.421479 CCGTCGCTCTTCGCCTGT 62.421 66.667 0.00 0.00 38.27 4.00
2377 13056 4.543736 CATCGTTCGCGCGTCTGC 62.544 66.667 30.98 16.42 41.05 4.26
2378 13057 3.902063 CCATCGTTCGCGCGTCTG 61.902 66.667 30.98 19.57 41.05 3.51
2427 13106 2.756283 ACCTCCTCTTCGGCCGAG 60.756 66.667 29.20 21.49 0.00 4.63
2428 13107 2.754658 GACCTCCTCTTCGGCCGA 60.755 66.667 27.28 27.28 0.00 5.54
2429 13108 4.194720 CGACCTCCTCTTCGGCCG 62.195 72.222 22.12 22.12 0.00 6.13
2433 13112 2.711922 CCACCCGACCTCCTCTTCG 61.712 68.421 0.00 0.00 34.93 3.79
2435 13114 1.609794 GACCACCCGACCTCCTCTT 60.610 63.158 0.00 0.00 0.00 2.85
2436 13115 2.037527 GACCACCCGACCTCCTCT 59.962 66.667 0.00 0.00 0.00 3.69
2437 13116 3.450115 CGACCACCCGACCTCCTC 61.450 72.222 0.00 0.00 0.00 3.71
2450 13129 4.409218 TACGACACTGGCGCGACC 62.409 66.667 10.82 11.50 39.84 4.79
2451 13130 2.244436 TACTACGACACTGGCGCGAC 62.244 60.000 12.10 8.22 0.00 5.19
2453 13132 1.582937 CTACTACGACACTGGCGCG 60.583 63.158 3.53 0.00 0.00 6.86
2456 13135 0.100861 GCCTCTACTACGACACTGGC 59.899 60.000 0.00 0.00 0.00 4.85
2460 13139 0.522915 GCGTGCCTCTACTACGACAC 60.523 60.000 0.00 0.00 40.01 3.67
2461 13140 1.798735 GCGTGCCTCTACTACGACA 59.201 57.895 0.00 0.00 40.01 4.35
2462 13141 1.297451 CGCGTGCCTCTACTACGAC 60.297 63.158 0.00 0.00 40.01 4.34
2463 13142 2.466982 CCGCGTGCCTCTACTACGA 61.467 63.158 4.92 0.00 40.01 3.43
2465 13144 2.412112 CCCGCGTGCCTCTACTAC 59.588 66.667 4.92 0.00 0.00 2.73
2466 13145 2.831742 CCCCGCGTGCCTCTACTA 60.832 66.667 4.92 0.00 0.00 1.82
2494 13173 4.090057 GTTTGAGTCGCCCGCAGC 62.090 66.667 0.00 0.00 38.52 5.25
2495 13174 3.423154 GGTTTGAGTCGCCCGCAG 61.423 66.667 0.00 0.00 0.00 5.18
2498 13177 3.110178 GTCGGTTTGAGTCGCCCG 61.110 66.667 8.24 8.24 41.75 6.13
2499 13178 2.741211 GGTCGGTTTGAGTCGCCC 60.741 66.667 0.00 0.00 0.00 6.13
2500 13179 2.476534 TACGGTCGGTTTGAGTCGCC 62.477 60.000 0.00 0.00 0.00 5.54
2501 13180 1.069378 CTACGGTCGGTTTGAGTCGC 61.069 60.000 0.00 0.00 0.00 5.19
2503 13182 2.790468 CGATCTACGGTCGGTTTGAGTC 60.790 54.545 0.00 0.00 38.46 3.36
2504 13183 1.131883 CGATCTACGGTCGGTTTGAGT 59.868 52.381 0.00 0.00 38.46 3.41
2505 13184 1.399440 TCGATCTACGGTCGGTTTGAG 59.601 52.381 0.00 0.00 42.82 3.02
2507 13186 2.486951 ATCGATCTACGGTCGGTTTG 57.513 50.000 0.00 0.00 42.82 2.93
2508 13187 4.354587 GTTTATCGATCTACGGTCGGTTT 58.645 43.478 0.00 0.00 42.82 3.27
2509 13188 3.243201 GGTTTATCGATCTACGGTCGGTT 60.243 47.826 0.00 0.00 42.82 4.44
2510 13189 2.291741 GGTTTATCGATCTACGGTCGGT 59.708 50.000 0.00 0.00 42.82 4.69
2511 13190 2.291465 TGGTTTATCGATCTACGGTCGG 59.709 50.000 0.00 0.00 42.82 4.79
2512 13191 3.614159 TGGTTTATCGATCTACGGTCG 57.386 47.619 0.00 0.00 42.82 4.79
2514 13193 6.400568 TCTTTTTGGTTTATCGATCTACGGT 58.599 36.000 0.00 0.00 42.82 4.83
2516 13195 9.601971 TTTTTCTTTTTGGTTTATCGATCTACG 57.398 29.630 0.00 0.00 44.09 3.51
2519 13198 7.114388 GCGTTTTTCTTTTTGGTTTATCGATCT 59.886 33.333 0.00 0.00 0.00 2.75
2520 13199 7.217880 GCGTTTTTCTTTTTGGTTTATCGATC 58.782 34.615 0.00 0.00 0.00 3.69
2521 13200 6.144886 GGCGTTTTTCTTTTTGGTTTATCGAT 59.855 34.615 2.16 2.16 0.00 3.59
2522 13201 5.459434 GGCGTTTTTCTTTTTGGTTTATCGA 59.541 36.000 0.00 0.00 0.00 3.59
2523 13202 5.608630 CGGCGTTTTTCTTTTTGGTTTATCG 60.609 40.000 0.00 0.00 0.00 2.92
2526 13205 4.741342 TCGGCGTTTTTCTTTTTGGTTTA 58.259 34.783 6.85 0.00 0.00 2.01
2527 13206 3.586892 TCGGCGTTTTTCTTTTTGGTTT 58.413 36.364 6.85 0.00 0.00 3.27
2528 13207 3.233684 TCGGCGTTTTTCTTTTTGGTT 57.766 38.095 6.85 0.00 0.00 3.67
2530 13209 3.376540 TGATCGGCGTTTTTCTTTTTGG 58.623 40.909 6.85 0.00 0.00 3.28
2531 13210 4.737765 TCTTGATCGGCGTTTTTCTTTTTG 59.262 37.500 6.85 0.00 0.00 2.44
2533 13212 4.287720 GTCTTGATCGGCGTTTTTCTTTT 58.712 39.130 6.85 0.00 0.00 2.27
2534 13213 3.606153 CGTCTTGATCGGCGTTTTTCTTT 60.606 43.478 6.85 0.00 0.00 2.52
2535 13214 2.096417 CGTCTTGATCGGCGTTTTTCTT 60.096 45.455 6.85 0.00 0.00 2.52
2536 13215 1.459592 CGTCTTGATCGGCGTTTTTCT 59.540 47.619 6.85 0.00 0.00 2.52
2537 13216 1.458064 TCGTCTTGATCGGCGTTTTTC 59.542 47.619 6.85 0.84 0.00 2.29
2538 13217 1.193874 GTCGTCTTGATCGGCGTTTTT 59.806 47.619 6.85 0.00 0.00 1.94
2540 13219 1.012486 GGTCGTCTTGATCGGCGTTT 61.012 55.000 6.85 0.00 33.53 3.60
2542 13221 2.181021 GGTCGTCTTGATCGGCGT 59.819 61.111 6.85 0.00 33.53 5.68
2547 13226 1.586564 CTCGCCGGTCGTCTTGATC 60.587 63.158 16.00 0.00 39.67 2.92
2548 13227 2.044555 TCTCGCCGGTCGTCTTGAT 61.045 57.895 16.00 0.00 39.67 2.57


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

AutoCloner maintained by Alex Coulton.