Multiple sequence alignment - TraesCS7D01G541000

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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 TraesCS7D01G541000 chr7D 100.000 3082 0 0 1 3082 630683638 630686719 0.000000e+00 5692.0
1 TraesCS7D01G541000 chr7D 94.759 1450 62 10 1 1443 631251523 631252965 0.000000e+00 2244.0
2 TraesCS7D01G541000 chr7D 90.965 819 70 4 2267 3082 267431288 267432105 0.000000e+00 1099.0
3 TraesCS7D01G541000 chr7D 90.223 583 34 10 1514 2074 631252974 631253555 0.000000e+00 739.0
4 TraesCS7D01G541000 chr7D 87.136 583 67 5 1232 1813 630833763 630833188 0.000000e+00 654.0
5 TraesCS7D01G541000 chr7D 87.136 583 67 5 1232 1813 631361197 631361772 0.000000e+00 654.0
6 TraesCS7D01G541000 chr7D 83.798 574 77 10 1230 1795 630678226 630678791 5.850000e-147 531.0
7 TraesCS7D01G541000 chr7D 89.157 166 14 3 337 500 454079409 454079246 1.450000e-48 204.0
8 TraesCS7D01G541000 chr7D 93.651 63 4 0 2012 2074 631253394 631253456 9.100000e-16 95.3
9 TraesCS7D01G541000 chr3D 92.176 818 57 4 2267 3082 537066744 537067556 0.000000e+00 1149.0
10 TraesCS7D01G541000 chr3D 90.876 822 63 10 2267 3082 327248740 327249555 0.000000e+00 1092.0
11 TraesCS7D01G541000 chr3D 90.709 818 72 4 2267 3082 314376733 314377548 0.000000e+00 1086.0
12 TraesCS7D01G541000 chr3D 83.898 118 14 5 1946 2060 589707612 589707727 1.170000e-19 108.0
13 TraesCS7D01G541000 chr5D 90.987 821 67 7 2267 3082 328287753 328288571 0.000000e+00 1099.0
14 TraesCS7D01G541000 chr5D 84.559 136 20 1 1928 2062 340103320 340103455 1.930000e-27 134.0
15 TraesCS7D01G541000 chr5D 75.839 149 22 11 1036 1177 443628291 443628150 2.570000e-06 63.9
16 TraesCS7D01G541000 chr1B 90.965 819 66 8 2267 3081 403819755 403818941 0.000000e+00 1096.0
17 TraesCS7D01G541000 chr1A 90.732 820 73 3 2266 3082 245248524 245249343 0.000000e+00 1090.0
18 TraesCS7D01G541000 chr1A 86.207 87 11 1 2114 2199 408070566 408070652 3.270000e-15 93.5
19 TraesCS7D01G541000 chr2D 90.610 820 71 6 2267 3082 255595104 255594287 0.000000e+00 1083.0
20 TraesCS7D01G541000 chr6D 90.587 818 71 6 2267 3082 371181708 371180895 0.000000e+00 1079.0
21 TraesCS7D01G541000 chr6D 86.905 84 8 3 933 1013 412724865 412724948 1.180000e-14 91.6
22 TraesCS7D01G541000 chr6D 84.211 76 11 1 937 1012 412477910 412477984 4.260000e-09 73.1
23 TraesCS7D01G541000 chrUn 83.130 575 79 12 1230 1795 88643203 88643768 2.740000e-140 508.0
24 TraesCS7D01G541000 chrUn 83.130 575 79 12 1230 1795 283733294 283733859 2.740000e-140 508.0
25 TraesCS7D01G541000 chrUn 85.401 137 11 7 1231 1358 364243352 364243216 1.930000e-27 134.0
26 TraesCS7D01G541000 chr7A 82.948 563 81 12 1230 1781 727038229 727037671 7.680000e-136 494.0
27 TraesCS7D01G541000 chr6B 90.909 165 13 1 337 499 583446147 583445983 1.440000e-53 220.0
28 TraesCS7D01G541000 chr6B 88.757 169 15 3 335 500 83138380 83138547 1.450000e-48 204.0
29 TraesCS7D01G541000 chr6B 88.690 168 14 4 335 499 36133500 36133665 1.870000e-47 200.0
30 TraesCS7D01G541000 chr6B 89.024 164 14 3 338 499 226361518 226361679 1.870000e-47 200.0
31 TraesCS7D01G541000 chr5A 89.697 165 13 3 337 499 320214406 320214244 1.120000e-49 207.0
32 TraesCS7D01G541000 chr3B 89.091 165 16 1 337 499 752695446 752695282 1.450000e-48 204.0
33 TraesCS7D01G541000 chr4D 89.024 164 14 3 338 499 479687421 479687260 1.870000e-47 200.0
34 TraesCS7D01G541000 chr4D 85.833 120 13 3 1947 2062 52830301 52830182 1.160000e-24 124.0
35 TraesCS7D01G541000 chr5B 82.353 170 27 3 1895 2062 554510213 554510381 8.910000e-31 145.0
36 TraesCS7D01G541000 chr5B 85.000 60 8 1 2204 2263 437806483 437806541 3.320000e-05 60.2
37 TraesCS7D01G541000 chr7B 79.263 217 31 12 1860 2073 179332586 179332791 4.140000e-29 139.0
38 TraesCS7D01G541000 chr7B 84.559 136 20 1 1928 2062 750052364 750052499 1.930000e-27 134.0
39 TraesCS7D01G541000 chr2B 87.611 113 13 1 1951 2062 38848172 38848060 2.490000e-26 130.0


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 TraesCS7D01G541000 chr7D 630683638 630686719 3081 False 5692.0 5692 100.000000 1 3082 1 chr7D.!!$F3 3081
1 TraesCS7D01G541000 chr7D 267431288 267432105 817 False 1099.0 1099 90.965000 2267 3082 1 chr7D.!!$F1 815
2 TraesCS7D01G541000 chr7D 631251523 631253555 2032 False 1026.1 2244 92.877667 1 2074 3 chr7D.!!$F5 2073
3 TraesCS7D01G541000 chr7D 630833188 630833763 575 True 654.0 654 87.136000 1232 1813 1 chr7D.!!$R2 581
4 TraesCS7D01G541000 chr7D 631361197 631361772 575 False 654.0 654 87.136000 1232 1813 1 chr7D.!!$F4 581
5 TraesCS7D01G541000 chr7D 630678226 630678791 565 False 531.0 531 83.798000 1230 1795 1 chr7D.!!$F2 565
6 TraesCS7D01G541000 chr3D 537066744 537067556 812 False 1149.0 1149 92.176000 2267 3082 1 chr3D.!!$F3 815
7 TraesCS7D01G541000 chr3D 327248740 327249555 815 False 1092.0 1092 90.876000 2267 3082 1 chr3D.!!$F2 815
8 TraesCS7D01G541000 chr3D 314376733 314377548 815 False 1086.0 1086 90.709000 2267 3082 1 chr3D.!!$F1 815
9 TraesCS7D01G541000 chr5D 328287753 328288571 818 False 1099.0 1099 90.987000 2267 3082 1 chr5D.!!$F1 815
10 TraesCS7D01G541000 chr1B 403818941 403819755 814 True 1096.0 1096 90.965000 2267 3081 1 chr1B.!!$R1 814
11 TraesCS7D01G541000 chr1A 245248524 245249343 819 False 1090.0 1090 90.732000 2266 3082 1 chr1A.!!$F1 816
12 TraesCS7D01G541000 chr2D 255594287 255595104 817 True 1083.0 1083 90.610000 2267 3082 1 chr2D.!!$R1 815
13 TraesCS7D01G541000 chr6D 371180895 371181708 813 True 1079.0 1079 90.587000 2267 3082 1 chr6D.!!$R1 815
14 TraesCS7D01G541000 chrUn 88643203 88643768 565 False 508.0 508 83.130000 1230 1795 1 chrUn.!!$F1 565
15 TraesCS7D01G541000 chrUn 283733294 283733859 565 False 508.0 508 83.130000 1230 1795 1 chrUn.!!$F2 565
16 TraesCS7D01G541000 chr7A 727037671 727038229 558 True 494.0 494 82.948000 1230 1781 1 chr7A.!!$R1 551

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
29 30 2.925724 TCGCAAAAAGAGGAAGGTTCA 58.074 42.857 0.00 0.0 0.00 3.18 F
1662 1680 0.394899 CTTCAGGAAGGGCATGGTCC 60.395 60.000 1.01 0.0 34.87 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 1926 0.681733 GAATGGGATAGCTCGCCAGA 59.318 55.0 7.05 0.0 33.54 3.86 R
2772 2826 0.178953 AGGGCAGCAAGGTTGATGTT 60.179 50.0 9.53 0.0 45.71 2.71 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
29 30 2.925724 TCGCAAAAAGAGGAAGGTTCA 58.074 42.857 0.00 0.00 0.00 3.18
173 175 6.067263 TCCCTTTATGAAGAAACAACAACG 57.933 37.500 0.00 0.00 34.71 4.10
178 180 8.318167 CCTTTATGAAGAAACAACAACGAAAAC 58.682 33.333 0.00 0.00 34.71 2.43
441 445 6.939163 AGTGTAGATTCACTCATTTTGCTTCT 59.061 34.615 0.00 0.00 44.07 2.85
496 500 7.578203 AGAGTTTTATTTAGGAATGGAGGGAG 58.422 38.462 0.00 0.00 0.00 4.30
552 556 8.695456 CCTAAAAAGGAATGTATTAGTGGCATT 58.305 33.333 0.00 0.00 35.78 3.56
759 763 9.063615 TGGTGTTAATCTTTAAGAAGAAAGGAC 57.936 33.333 0.00 0.00 44.61 3.85
1245 1253 2.202987 GCATCTGCTGGGAGTCCG 60.203 66.667 2.26 0.00 38.21 4.79
1297 1305 2.502692 AAGAAGGTAGTCGCCCACGC 62.503 60.000 0.00 0.00 39.84 5.34
1298 1306 2.995574 AAGGTAGTCGCCCACGCT 60.996 61.111 0.00 0.00 39.84 5.07
1445 1462 1.346068 GACAAGGTGCTCTTCCTCAGT 59.654 52.381 0.00 0.00 33.76 3.41
1469 1486 4.819761 GAGATGCTGCGCGACCCA 62.820 66.667 12.10 2.24 0.00 4.51
1504 1522 4.329545 GCTGGTGCGGTTCCTGGA 62.330 66.667 0.00 0.00 0.00 3.86
1518 1536 3.220999 CTGGAGTGCCCGTTCACGA 62.221 63.158 0.00 0.00 43.02 4.35
1662 1680 0.394899 CTTCAGGAAGGGCATGGTCC 60.395 60.000 1.01 0.00 34.87 4.46
1677 1695 4.717629 TCCGCGACTGGAGCAACG 62.718 66.667 8.23 0.00 33.05 4.10
1791 1809 1.219393 GAAGAAGGTGCTCCTCCGG 59.781 63.158 7.99 0.00 44.35 5.14
1807 1825 2.202892 GGAGATCGGTTGACGGGC 60.203 66.667 0.00 0.00 44.45 6.13
1827 1845 4.210328 GGGCGAAAGTTTTTATTGTGTTGG 59.790 41.667 0.00 0.00 0.00 3.77
1872 1890 0.883833 TACTATAAGGGCGCGCTACC 59.116 55.000 32.29 24.42 0.00 3.18
1893 1912 2.739913 CGGTCGGCAACTGATTCTTTTA 59.260 45.455 0.00 0.00 36.22 1.52
1901 1920 7.807907 TCGGCAACTGATTCTTTTAAAAAGATC 59.192 33.333 1.66 8.68 0.00 2.75
1907 1926 7.172703 ACTGATTCTTTTAAAAAGATCCGTCGT 59.827 33.333 15.31 8.39 0.00 4.34
1926 1945 0.681733 TCTGGCGAGCTATCCCATTC 59.318 55.000 0.00 0.00 0.00 2.67
1927 1946 0.683973 CTGGCGAGCTATCCCATTCT 59.316 55.000 0.00 0.00 0.00 2.40
1938 1957 2.890808 TCCCATTCTGTGATACGAGC 57.109 50.000 0.00 0.00 0.00 5.03
1939 1958 1.412710 TCCCATTCTGTGATACGAGCC 59.587 52.381 0.00 0.00 0.00 4.70
1940 1959 1.138859 CCCATTCTGTGATACGAGCCA 59.861 52.381 0.00 0.00 0.00 4.75
1942 1961 3.062763 CCATTCTGTGATACGAGCCATC 58.937 50.000 0.00 0.00 0.00 3.51
1943 1962 3.493176 CCATTCTGTGATACGAGCCATCA 60.493 47.826 0.00 0.00 0.00 3.07
1944 1963 3.885724 TTCTGTGATACGAGCCATCAA 57.114 42.857 0.00 0.00 34.32 2.57
1945 1964 4.406648 TTCTGTGATACGAGCCATCAAT 57.593 40.909 0.00 0.00 34.32 2.57
1947 1966 4.769688 TCTGTGATACGAGCCATCAATTT 58.230 39.130 0.00 0.00 34.32 1.82
1950 1978 5.185454 TGTGATACGAGCCATCAATTTCTT 58.815 37.500 0.00 0.00 34.32 2.52
2074 2114 4.036262 TGCAACAAGTCACCTGTTACAATC 59.964 41.667 0.00 0.00 0.00 2.67
2075 2115 4.275936 GCAACAAGTCACCTGTTACAATCT 59.724 41.667 0.00 0.00 0.00 2.40
2076 2116 5.221048 GCAACAAGTCACCTGTTACAATCTT 60.221 40.000 0.00 0.00 0.00 2.40
2077 2117 6.430451 CAACAAGTCACCTGTTACAATCTTC 58.570 40.000 0.00 0.00 0.00 2.87
2078 2118 4.750098 ACAAGTCACCTGTTACAATCTTCG 59.250 41.667 0.00 0.00 0.00 3.79
2079 2119 3.326747 AGTCACCTGTTACAATCTTCGC 58.673 45.455 0.00 0.00 0.00 4.70
2080 2120 2.415512 GTCACCTGTTACAATCTTCGCC 59.584 50.000 0.00 0.00 0.00 5.54
2081 2121 2.037902 TCACCTGTTACAATCTTCGCCA 59.962 45.455 0.00 0.00 0.00 5.69
2082 2122 2.811431 CACCTGTTACAATCTTCGCCAA 59.189 45.455 0.00 0.00 0.00 4.52
2083 2123 3.252215 CACCTGTTACAATCTTCGCCAAA 59.748 43.478 0.00 0.00 0.00 3.28
2084 2124 3.886505 ACCTGTTACAATCTTCGCCAAAA 59.113 39.130 0.00 0.00 0.00 2.44
2085 2125 4.339814 ACCTGTTACAATCTTCGCCAAAAA 59.660 37.500 0.00 0.00 0.00 1.94
2108 2148 5.830000 AAGTCAACTGTTACAAAACCTCC 57.170 39.130 0.00 0.00 34.49 4.30
2109 2149 5.112129 AGTCAACTGTTACAAAACCTCCT 57.888 39.130 0.00 0.00 34.49 3.69
2110 2150 5.123936 AGTCAACTGTTACAAAACCTCCTC 58.876 41.667 0.00 0.00 34.49 3.71
2111 2151 5.104485 AGTCAACTGTTACAAAACCTCCTCT 60.104 40.000 0.00 0.00 34.49 3.69
2112 2152 5.589050 GTCAACTGTTACAAAACCTCCTCTT 59.411 40.000 0.00 0.00 34.49 2.85
2113 2153 6.095021 GTCAACTGTTACAAAACCTCCTCTTT 59.905 38.462 0.00 0.00 34.49 2.52
2114 2154 6.317893 TCAACTGTTACAAAACCTCCTCTTTC 59.682 38.462 0.00 0.00 34.49 2.62
2115 2155 6.002653 ACTGTTACAAAACCTCCTCTTTCT 57.997 37.500 0.00 0.00 34.49 2.52
2116 2156 7.133133 ACTGTTACAAAACCTCCTCTTTCTA 57.867 36.000 0.00 0.00 34.49 2.10
2117 2157 7.571025 ACTGTTACAAAACCTCCTCTTTCTAA 58.429 34.615 0.00 0.00 34.49 2.10
2118 2158 8.218488 ACTGTTACAAAACCTCCTCTTTCTAAT 58.782 33.333 0.00 0.00 34.49 1.73
2119 2159 8.990163 TGTTACAAAACCTCCTCTTTCTAATT 57.010 30.769 0.00 0.00 34.49 1.40
2120 2160 9.416284 TGTTACAAAACCTCCTCTTTCTAATTT 57.584 29.630 0.00 0.00 34.49 1.82
2143 2183 7.899648 TTTTTATAACAAGACCCTTGTGGAA 57.100 32.000 12.42 5.50 38.00 3.53
2144 2184 7.899648 TTTTATAACAAGACCCTTGTGGAAA 57.100 32.000 12.42 10.14 38.00 3.13
2145 2185 7.899648 TTTATAACAAGACCCTTGTGGAAAA 57.100 32.000 12.42 10.01 38.00 2.29
2146 2186 7.899648 TTATAACAAGACCCTTGTGGAAAAA 57.100 32.000 12.42 2.50 38.00 1.94
2147 2187 6.994421 ATAACAAGACCCTTGTGGAAAAAT 57.006 33.333 12.42 0.00 38.00 1.82
2148 2188 5.692115 AACAAGACCCTTGTGGAAAAATT 57.308 34.783 12.42 0.00 38.00 1.82
2149 2189 5.022282 ACAAGACCCTTGTGGAAAAATTG 57.978 39.130 11.10 0.00 38.00 2.32
2150 2190 3.751479 AGACCCTTGTGGAAAAATTGC 57.249 42.857 0.00 0.00 38.00 3.56
2151 2191 3.037549 AGACCCTTGTGGAAAAATTGCA 58.962 40.909 0.00 0.00 38.00 4.08
2152 2192 3.454082 AGACCCTTGTGGAAAAATTGCAA 59.546 39.130 0.00 0.00 38.00 4.08
2153 2193 4.102996 AGACCCTTGTGGAAAAATTGCAAT 59.897 37.500 5.99 5.99 38.00 3.56
2154 2194 5.306678 AGACCCTTGTGGAAAAATTGCAATA 59.693 36.000 13.39 0.00 38.00 1.90
2155 2195 5.934781 ACCCTTGTGGAAAAATTGCAATAA 58.065 33.333 13.39 0.00 38.00 1.40
2156 2196 5.762711 ACCCTTGTGGAAAAATTGCAATAAC 59.237 36.000 13.39 5.51 38.00 1.89
2157 2197 5.762218 CCCTTGTGGAAAAATTGCAATAACA 59.238 36.000 13.39 7.92 35.39 2.41
2158 2198 6.430616 CCCTTGTGGAAAAATTGCAATAACAT 59.569 34.615 13.39 0.00 35.39 2.71
2159 2199 7.361116 CCCTTGTGGAAAAATTGCAATAACATC 60.361 37.037 13.39 8.85 35.39 3.06
2160 2200 7.388500 CCTTGTGGAAAAATTGCAATAACATCT 59.612 33.333 13.39 0.00 34.57 2.90
2161 2201 7.887996 TGTGGAAAAATTGCAATAACATCTC 57.112 32.000 13.39 4.14 30.97 2.75
2162 2202 6.873076 TGTGGAAAAATTGCAATAACATCTCC 59.127 34.615 13.39 12.80 30.97 3.71
2163 2203 6.034898 GTGGAAAAATTGCAATAACATCTCCG 59.965 38.462 13.39 0.00 30.97 4.63
2164 2204 5.519927 GGAAAAATTGCAATAACATCTCCGG 59.480 40.000 13.39 0.00 0.00 5.14
2165 2205 3.715628 AATTGCAATAACATCTCCGGC 57.284 42.857 13.39 0.00 0.00 6.13
2166 2206 1.388547 TTGCAATAACATCTCCGGCC 58.611 50.000 0.00 0.00 0.00 6.13
2167 2207 0.813610 TGCAATAACATCTCCGGCCG 60.814 55.000 21.04 21.04 0.00 6.13
2168 2208 1.941812 CAATAACATCTCCGGCCGC 59.058 57.895 22.85 0.00 0.00 6.53
2169 2209 0.813610 CAATAACATCTCCGGCCGCA 60.814 55.000 22.85 2.88 0.00 5.69
2170 2210 0.108585 AATAACATCTCCGGCCGCAT 59.891 50.000 22.85 8.27 0.00 4.73
2171 2211 0.320771 ATAACATCTCCGGCCGCATC 60.321 55.000 22.85 0.00 0.00 3.91
2172 2212 1.681486 TAACATCTCCGGCCGCATCA 61.681 55.000 22.85 2.69 0.00 3.07
2173 2213 2.969238 CATCTCCGGCCGCATCAC 60.969 66.667 22.85 0.00 0.00 3.06
2174 2214 3.469970 ATCTCCGGCCGCATCACA 61.470 61.111 22.85 0.00 0.00 3.58
2175 2215 3.740128 ATCTCCGGCCGCATCACAC 62.740 63.158 22.85 0.00 0.00 3.82
2176 2216 4.758251 CTCCGGCCGCATCACACA 62.758 66.667 22.85 0.00 0.00 3.72
2179 2219 2.125713 CGGCCGCATCACACACTA 60.126 61.111 14.67 0.00 0.00 2.74
2180 2220 1.739929 CGGCCGCATCACACACTAA 60.740 57.895 14.67 0.00 0.00 2.24
2181 2221 1.794222 GGCCGCATCACACACTAAC 59.206 57.895 0.00 0.00 0.00 2.34
2182 2222 0.953471 GGCCGCATCACACACTAACA 60.953 55.000 0.00 0.00 0.00 2.41
2183 2223 1.086696 GCCGCATCACACACTAACAT 58.913 50.000 0.00 0.00 0.00 2.71
2184 2224 2.276201 GCCGCATCACACACTAACATA 58.724 47.619 0.00 0.00 0.00 2.29
2185 2225 2.285220 GCCGCATCACACACTAACATAG 59.715 50.000 0.00 0.00 0.00 2.23
2186 2226 3.521560 CCGCATCACACACTAACATAGT 58.478 45.455 0.00 0.00 40.28 2.12
2187 2227 3.551890 CCGCATCACACACTAACATAGTC 59.448 47.826 0.00 0.00 36.76 2.59
2188 2228 3.240631 CGCATCACACACTAACATAGTCG 59.759 47.826 0.00 0.00 36.76 4.18
2189 2229 4.174009 GCATCACACACTAACATAGTCGT 58.826 43.478 0.00 0.00 36.76 4.34
2190 2230 4.265556 GCATCACACACTAACATAGTCGTC 59.734 45.833 0.00 0.00 36.76 4.20
2191 2231 5.641709 CATCACACACTAACATAGTCGTCT 58.358 41.667 0.00 0.00 36.76 4.18
2192 2232 5.700722 TCACACACTAACATAGTCGTCTT 57.299 39.130 0.00 0.00 36.76 3.01
2193 2233 6.080648 TCACACACTAACATAGTCGTCTTT 57.919 37.500 0.00 0.00 36.76 2.52
2194 2234 6.147581 TCACACACTAACATAGTCGTCTTTC 58.852 40.000 0.00 0.00 36.76 2.62
2195 2235 5.059343 CACACACTAACATAGTCGTCTTTCG 59.941 44.000 0.00 0.00 36.76 3.46
2196 2236 4.030306 CACACTAACATAGTCGTCTTTCGC 59.970 45.833 0.00 0.00 36.76 4.70
2197 2237 4.082895 ACACTAACATAGTCGTCTTTCGCT 60.083 41.667 0.00 0.00 36.76 4.93
2198 2238 4.263209 CACTAACATAGTCGTCTTTCGCTG 59.737 45.833 0.00 0.00 36.76 5.18
2199 2239 1.630148 ACATAGTCGTCTTTCGCTGC 58.370 50.000 0.00 0.00 39.67 5.25
2200 2240 0.924090 CATAGTCGTCTTTCGCTGCC 59.076 55.000 0.00 0.00 39.67 4.85
2201 2241 0.525668 ATAGTCGTCTTTCGCTGCCG 60.526 55.000 0.00 0.00 39.67 5.69
2202 2242 1.579964 TAGTCGTCTTTCGCTGCCGA 61.580 55.000 0.00 0.00 42.66 5.54
2203 2243 1.805945 GTCGTCTTTCGCTGCCGAT 60.806 57.895 0.00 0.00 43.97 4.18
2204 2244 1.805539 TCGTCTTTCGCTGCCGATG 60.806 57.895 0.00 0.00 43.97 3.84
2205 2245 2.094659 CGTCTTTCGCTGCCGATGT 61.095 57.895 0.00 0.00 43.97 3.06
2206 2246 1.626654 CGTCTTTCGCTGCCGATGTT 61.627 55.000 0.00 0.00 43.97 2.71
2207 2247 0.179215 GTCTTTCGCTGCCGATGTTG 60.179 55.000 0.00 0.00 43.97 3.33
2208 2248 0.602638 TCTTTCGCTGCCGATGTTGT 60.603 50.000 0.00 0.00 43.97 3.32
2209 2249 0.238289 CTTTCGCTGCCGATGTTGTT 59.762 50.000 0.00 0.00 43.97 2.83
2210 2250 0.040514 TTTCGCTGCCGATGTTGTTG 60.041 50.000 0.00 0.00 43.97 3.33
2211 2251 2.456594 TTCGCTGCCGATGTTGTTGC 62.457 55.000 0.00 0.00 43.97 4.17
2212 2252 2.644418 GCTGCCGATGTTGTTGCA 59.356 55.556 0.00 0.00 0.00 4.08
2213 2253 4.853507 CTGCCGATGTTGTTGCAG 57.146 55.556 0.00 0.00 44.43 4.41
2214 2254 4.471761 TGCCGATGTTGTTGCAGA 57.528 50.000 0.00 0.00 0.00 4.26
2215 2255 2.712984 TGCCGATGTTGTTGCAGAA 58.287 47.368 0.00 0.00 0.00 3.02
2216 2256 1.028130 TGCCGATGTTGTTGCAGAAA 58.972 45.000 0.00 0.00 0.00 2.52
2217 2257 1.268999 TGCCGATGTTGTTGCAGAAAC 60.269 47.619 6.63 6.63 39.41 2.78
2218 2258 1.001378 GCCGATGTTGTTGCAGAAACT 60.001 47.619 12.97 1.83 39.70 2.66
2219 2259 2.543653 GCCGATGTTGTTGCAGAAACTT 60.544 45.455 12.97 7.98 39.70 2.66
2220 2260 3.044986 CCGATGTTGTTGCAGAAACTTG 58.955 45.455 12.97 4.96 39.70 3.16
2221 2261 3.044986 CGATGTTGTTGCAGAAACTTGG 58.955 45.455 12.97 6.25 39.70 3.61
2222 2262 3.243035 CGATGTTGTTGCAGAAACTTGGA 60.243 43.478 12.97 0.00 39.70 3.53
2223 2263 3.781079 TGTTGTTGCAGAAACTTGGAG 57.219 42.857 12.97 0.00 39.70 3.86
2224 2264 3.088532 TGTTGTTGCAGAAACTTGGAGT 58.911 40.909 12.97 0.00 39.70 3.85
2225 2265 3.119531 TGTTGTTGCAGAAACTTGGAGTG 60.120 43.478 12.97 0.00 39.70 3.51
2226 2266 2.023673 TGTTGCAGAAACTTGGAGTGG 58.976 47.619 0.00 0.00 39.70 4.00
2227 2267 2.297701 GTTGCAGAAACTTGGAGTGGA 58.702 47.619 0.00 0.00 35.75 4.02
2228 2268 1.967319 TGCAGAAACTTGGAGTGGAC 58.033 50.000 0.00 0.00 0.00 4.02
2229 2269 0.868406 GCAGAAACTTGGAGTGGACG 59.132 55.000 0.00 0.00 0.00 4.79
2230 2270 1.810412 GCAGAAACTTGGAGTGGACGT 60.810 52.381 0.00 0.00 0.00 4.34
2231 2271 1.867233 CAGAAACTTGGAGTGGACGTG 59.133 52.381 0.00 0.00 0.00 4.49
2232 2272 1.202651 AGAAACTTGGAGTGGACGTGG 60.203 52.381 0.00 0.00 0.00 4.94
2233 2273 0.834612 AAACTTGGAGTGGACGTGGA 59.165 50.000 0.00 0.00 0.00 4.02
2234 2274 0.106149 AACTTGGAGTGGACGTGGAC 59.894 55.000 0.00 0.00 0.00 4.02
2235 2275 1.046472 ACTTGGAGTGGACGTGGACA 61.046 55.000 0.00 0.00 0.00 4.02
2236 2276 0.321671 CTTGGAGTGGACGTGGACAT 59.678 55.000 0.00 0.00 0.00 3.06
2237 2277 1.548719 CTTGGAGTGGACGTGGACATA 59.451 52.381 0.00 0.00 0.00 2.29
2238 2278 0.892755 TGGAGTGGACGTGGACATAC 59.107 55.000 0.00 0.00 0.00 2.39
2239 2279 0.892755 GGAGTGGACGTGGACATACA 59.107 55.000 0.00 0.00 0.00 2.29
2240 2280 1.480954 GGAGTGGACGTGGACATACAT 59.519 52.381 0.00 0.00 0.00 2.29
2241 2281 2.481449 GGAGTGGACGTGGACATACATC 60.481 54.545 0.00 0.00 0.00 3.06
2242 2282 2.165641 GAGTGGACGTGGACATACATCA 59.834 50.000 0.00 0.00 0.00 3.07
2243 2283 2.766263 AGTGGACGTGGACATACATCAT 59.234 45.455 0.00 0.00 0.00 2.45
2244 2284 2.866156 GTGGACGTGGACATACATCATG 59.134 50.000 0.00 0.00 40.78 3.07
2245 2285 2.158971 TGGACGTGGACATACATCATGG 60.159 50.000 0.00 0.00 39.13 3.66
2246 2286 2.158957 GGACGTGGACATACATCATGGT 60.159 50.000 0.00 0.00 39.13 3.55
2247 2287 2.866156 GACGTGGACATACATCATGGTG 59.134 50.000 3.86 3.86 39.13 4.17
2248 2288 2.499693 ACGTGGACATACATCATGGTGA 59.500 45.455 14.29 0.00 39.13 4.02
2249 2289 2.866156 CGTGGACATACATCATGGTGAC 59.134 50.000 14.29 0.00 39.13 3.67
2250 2290 2.866156 GTGGACATACATCATGGTGACG 59.134 50.000 14.29 2.70 39.13 4.35
2251 2291 2.499693 TGGACATACATCATGGTGACGT 59.500 45.455 14.29 6.17 39.13 4.34
2258 2298 2.359107 CATGGTGACGTGGCTGCT 60.359 61.111 0.00 0.00 43.88 4.24
2259 2299 1.079197 CATGGTGACGTGGCTGCTA 60.079 57.895 0.00 0.00 43.88 3.49
2260 2300 1.079127 ATGGTGACGTGGCTGCTAC 60.079 57.895 6.02 6.02 0.00 3.58
2261 2301 1.544825 ATGGTGACGTGGCTGCTACT 61.545 55.000 14.29 1.44 0.00 2.57
2262 2302 0.896479 TGGTGACGTGGCTGCTACTA 60.896 55.000 14.29 0.00 0.00 1.82
2263 2303 0.458025 GGTGACGTGGCTGCTACTAC 60.458 60.000 14.29 9.84 0.00 2.73
2264 2304 0.797249 GTGACGTGGCTGCTACTACG 60.797 60.000 14.29 14.16 41.86 3.51
2281 2321 0.529378 ACGGTGATACGTCTCCAACC 59.471 55.000 0.00 0.00 45.08 3.77
2772 2826 1.326951 TTCGATCACGGAGGGCATCA 61.327 55.000 0.08 0.00 40.21 3.07
2843 2898 5.618616 ACCTAAGGGTCCATAGCTAGTAT 57.381 43.478 0.00 0.00 43.38 2.12
2851 2906 6.448714 AGGGTCCATAGCTAGTATCTAGATGA 59.551 42.308 15.79 0.00 0.00 2.92
2865 2920 8.713971 AGTATCTAGATGACTTCTTCTCTCTCA 58.286 37.037 15.79 0.00 35.79 3.27
2888 2943 8.812513 TCAATGATCTTCAATACCATGTTCTT 57.187 30.769 0.00 0.00 0.00 2.52
3059 3114 6.532657 TGTATTTCTCTTCGAATTACCGGTTC 59.467 38.462 15.04 2.84 37.53 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.360370 TGCAACTAACTCACTCCTTCTTAT 57.640 37.500 0.00 0.00 0.00 1.73
212 214 6.818281 AGGGTAATACCAATTGCACTAGTA 57.182 37.500 12.03 0.00 39.39 1.82
374 378 5.011738 ACATCCGTATGTAGTCCCTTATTGG 59.988 44.000 0.00 0.00 44.66 3.16
470 474 7.939781 TCCCTCCATTCCTAAATAAAACTCTT 58.060 34.615 0.00 0.00 0.00 2.85
471 475 7.184753 ACTCCCTCCATTCCTAAATAAAACTCT 59.815 37.037 0.00 0.00 0.00 3.24
477 481 5.850028 CCCTACTCCCTCCATTCCTAAATAA 59.150 44.000 0.00 0.00 0.00 1.40
496 500 9.114952 CTTCCTTTTCTATGAGAATTTCCCTAC 57.885 37.037 0.00 0.00 33.67 3.18
531 535 5.957774 ACCAATGCCACTAATACATTCCTTT 59.042 36.000 0.00 0.00 31.82 3.11
535 539 8.512138 GGTATTACCAATGCCACTAATACATTC 58.488 37.037 8.03 0.00 42.52 2.67
630 634 8.396619 AGGGTAATACCAAAGGTACTAATTCA 57.603 34.615 12.03 0.00 41.31 2.57
985 992 7.639378 TCTTCTTAAAGGGTATGCCACTAATT 58.361 34.615 1.04 0.00 36.17 1.40
1037 1044 7.603963 TCTTCGCATACTATTAAAAAGTGCA 57.396 32.000 4.52 0.00 0.00 4.57
1127 1134 7.829224 TGATCTATGGGTATATTTGGGATGT 57.171 36.000 0.00 0.00 0.00 3.06
1228 1236 2.202987 CGGACTCCCAGCAGATGC 60.203 66.667 0.00 0.00 42.49 3.91
1236 1244 2.675423 CACGTCCTCGGACTCCCA 60.675 66.667 13.74 0.00 42.54 4.37
1245 1253 1.469940 CCATGACACTAGCACGTCCTC 60.470 57.143 0.00 0.00 0.00 3.71
1492 1509 4.329545 GGCACTCCAGGAACCGCA 62.330 66.667 6.72 0.00 0.00 5.69
1518 1536 2.444895 GGCATCCTCCTCCTCCGT 60.445 66.667 0.00 0.00 0.00 4.69
1621 1639 1.299926 GCGACGTTGGAGTCAGTGT 60.300 57.895 4.64 0.00 40.98 3.55
1662 1680 3.470567 GTCGTTGCTCCAGTCGCG 61.471 66.667 0.00 0.00 0.00 5.87
1791 1809 2.552585 TTCGCCCGTCAACCGATCTC 62.553 60.000 0.00 0.00 39.56 2.75
1807 1825 7.692908 ATCACCAACACAATAAAAACTTTCG 57.307 32.000 0.00 0.00 0.00 3.46
1849 1867 4.516698 GGTAGCGCGCCCTTATAGTATATA 59.483 45.833 30.33 5.51 0.00 0.86
1872 1890 1.156736 AAAGAATCAGTTGCCGACCG 58.843 50.000 0.00 0.00 0.00 4.79
1893 1912 1.439679 GCCAGACGACGGATCTTTTT 58.560 50.000 0.00 0.00 0.00 1.94
1907 1926 0.681733 GAATGGGATAGCTCGCCAGA 59.318 55.000 7.05 0.00 33.54 3.86
1926 1945 4.813161 AGAAATTGATGGCTCGTATCACAG 59.187 41.667 0.00 0.00 34.50 3.66
1927 1946 4.769688 AGAAATTGATGGCTCGTATCACA 58.230 39.130 0.00 0.00 34.50 3.58
1945 1964 9.868277 TTGTTGCAGAAAATTAGAGAAAAGAAA 57.132 25.926 0.00 0.00 0.00 2.52
1973 2001 7.340487 AGAGAAGAGGATGTTTTCAACAAAAGT 59.660 33.333 0.00 0.00 45.86 2.66
2083 2123 7.039293 AGGAGGTTTTGTAACAGTTGACTTTTT 60.039 33.333 0.00 0.00 35.92 1.94
2084 2124 6.436218 AGGAGGTTTTGTAACAGTTGACTTTT 59.564 34.615 0.00 0.00 35.92 2.27
2085 2125 5.949952 AGGAGGTTTTGTAACAGTTGACTTT 59.050 36.000 0.00 0.00 35.92 2.66
2086 2126 5.506708 AGGAGGTTTTGTAACAGTTGACTT 58.493 37.500 0.00 0.00 35.92 3.01
2087 2127 5.104485 AGAGGAGGTTTTGTAACAGTTGACT 60.104 40.000 0.00 0.00 35.92 3.41
2088 2128 5.123936 AGAGGAGGTTTTGTAACAGTTGAC 58.876 41.667 0.00 0.00 35.92 3.18
2089 2129 5.367945 AGAGGAGGTTTTGTAACAGTTGA 57.632 39.130 0.00 0.00 35.92 3.18
2090 2130 6.318900 AGAAAGAGGAGGTTTTGTAACAGTTG 59.681 38.462 0.00 0.00 35.92 3.16
2091 2131 6.424032 AGAAAGAGGAGGTTTTGTAACAGTT 58.576 36.000 0.00 0.00 35.92 3.16
2092 2132 6.002653 AGAAAGAGGAGGTTTTGTAACAGT 57.997 37.500 0.00 0.00 35.92 3.55
2093 2133 8.622948 ATTAGAAAGAGGAGGTTTTGTAACAG 57.377 34.615 0.00 0.00 35.92 3.16
2094 2134 8.990163 AATTAGAAAGAGGAGGTTTTGTAACA 57.010 30.769 0.00 0.00 35.92 2.41
2119 2159 7.899648 TTCCACAAGGGTCTTGTTATAAAAA 57.100 32.000 10.21 0.00 38.11 1.94
2120 2160 7.899648 TTTCCACAAGGGTCTTGTTATAAAA 57.100 32.000 10.21 6.57 38.11 1.52
2121 2161 7.899648 TTTTCCACAAGGGTCTTGTTATAAA 57.100 32.000 10.21 8.49 38.11 1.40
2122 2162 7.899648 TTTTTCCACAAGGGTCTTGTTATAA 57.100 32.000 10.21 3.67 38.11 0.98
2123 2163 8.364142 CAATTTTTCCACAAGGGTCTTGTTATA 58.636 33.333 10.21 0.00 38.11 0.98
2124 2164 6.994421 ATTTTTCCACAAGGGTCTTGTTAT 57.006 33.333 10.21 0.00 38.11 1.89
2125 2165 6.578023 CAATTTTTCCACAAGGGTCTTGTTA 58.422 36.000 10.21 0.58 38.11 2.41
2126 2166 5.427378 CAATTTTTCCACAAGGGTCTTGTT 58.573 37.500 10.21 0.00 38.11 2.83
2127 2167 4.683129 GCAATTTTTCCACAAGGGTCTTGT 60.683 41.667 7.41 7.41 38.11 3.16
2128 2168 3.809279 GCAATTTTTCCACAAGGGTCTTG 59.191 43.478 6.15 6.15 38.11 3.02
2129 2169 3.454082 TGCAATTTTTCCACAAGGGTCTT 59.546 39.130 0.00 0.00 38.11 3.01
2130 2170 3.037549 TGCAATTTTTCCACAAGGGTCT 58.962 40.909 0.00 0.00 38.11 3.85
2131 2171 3.467374 TGCAATTTTTCCACAAGGGTC 57.533 42.857 0.00 0.00 38.11 4.46
2132 2172 3.922171 TTGCAATTTTTCCACAAGGGT 57.078 38.095 0.00 0.00 38.11 4.34
2133 2173 5.762218 TGTTATTGCAATTTTTCCACAAGGG 59.238 36.000 18.75 0.00 34.83 3.95
2134 2174 6.857777 TGTTATTGCAATTTTTCCACAAGG 57.142 33.333 18.75 0.00 0.00 3.61
2135 2175 8.314143 AGATGTTATTGCAATTTTTCCACAAG 57.686 30.769 18.75 0.00 0.00 3.16
2136 2176 7.387397 GGAGATGTTATTGCAATTTTTCCACAA 59.613 33.333 18.75 0.00 0.00 3.33
2137 2177 6.873076 GGAGATGTTATTGCAATTTTTCCACA 59.127 34.615 18.75 11.11 0.00 4.17
2138 2178 6.034898 CGGAGATGTTATTGCAATTTTTCCAC 59.965 38.462 18.75 6.02 0.00 4.02
2139 2179 6.098679 CGGAGATGTTATTGCAATTTTTCCA 58.901 36.000 18.75 7.81 0.00 3.53
2140 2180 5.519927 CCGGAGATGTTATTGCAATTTTTCC 59.480 40.000 18.75 14.19 0.00 3.13
2141 2181 5.005682 GCCGGAGATGTTATTGCAATTTTTC 59.994 40.000 18.75 9.80 0.00 2.29
2142 2182 4.869861 GCCGGAGATGTTATTGCAATTTTT 59.130 37.500 18.75 0.27 0.00 1.94
2143 2183 4.432712 GCCGGAGATGTTATTGCAATTTT 58.567 39.130 18.75 0.00 0.00 1.82
2144 2184 3.181476 GGCCGGAGATGTTATTGCAATTT 60.181 43.478 18.75 0.00 0.00 1.82
2145 2185 2.362077 GGCCGGAGATGTTATTGCAATT 59.638 45.455 18.75 0.00 0.00 2.32
2146 2186 1.956477 GGCCGGAGATGTTATTGCAAT 59.044 47.619 17.56 17.56 0.00 3.56
2147 2187 1.388547 GGCCGGAGATGTTATTGCAA 58.611 50.000 5.05 0.00 0.00 4.08
2148 2188 0.813610 CGGCCGGAGATGTTATTGCA 60.814 55.000 20.10 0.00 0.00 4.08
2149 2189 1.941812 CGGCCGGAGATGTTATTGC 59.058 57.895 20.10 0.00 0.00 3.56
2150 2190 0.813610 TGCGGCCGGAGATGTTATTG 60.814 55.000 29.38 0.00 0.00 1.90
2151 2191 0.108585 ATGCGGCCGGAGATGTTATT 59.891 50.000 29.38 2.58 0.00 1.40
2152 2192 0.320771 GATGCGGCCGGAGATGTTAT 60.321 55.000 29.38 6.87 0.00 1.89
2153 2193 1.069090 GATGCGGCCGGAGATGTTA 59.931 57.895 29.38 0.00 0.00 2.41
2154 2194 2.203070 GATGCGGCCGGAGATGTT 60.203 61.111 29.38 8.72 0.00 2.71
2155 2195 3.469970 TGATGCGGCCGGAGATGT 61.470 61.111 29.38 9.20 0.00 3.06
2156 2196 2.969238 GTGATGCGGCCGGAGATG 60.969 66.667 29.38 0.00 0.00 2.90
2157 2197 3.469970 TGTGATGCGGCCGGAGAT 61.470 61.111 29.38 10.61 0.00 2.75
2158 2198 4.451150 GTGTGATGCGGCCGGAGA 62.451 66.667 29.38 12.70 0.00 3.71
2159 2199 4.758251 TGTGTGATGCGGCCGGAG 62.758 66.667 29.38 0.00 0.00 4.63
2161 2201 3.657448 TAGTGTGTGATGCGGCCGG 62.657 63.158 29.38 8.95 0.00 6.13
2162 2202 1.739929 TTAGTGTGTGATGCGGCCG 60.740 57.895 24.05 24.05 0.00 6.13
2163 2203 0.953471 TGTTAGTGTGTGATGCGGCC 60.953 55.000 0.00 0.00 0.00 6.13
2164 2204 1.086696 ATGTTAGTGTGTGATGCGGC 58.913 50.000 0.00 0.00 0.00 6.53
2165 2205 3.521560 ACTATGTTAGTGTGTGATGCGG 58.478 45.455 0.00 0.00 37.69 5.69
2166 2206 3.240631 CGACTATGTTAGTGTGTGATGCG 59.759 47.826 0.00 0.00 39.59 4.73
2167 2207 4.174009 ACGACTATGTTAGTGTGTGATGC 58.826 43.478 0.00 0.00 39.59 3.91
2168 2208 5.641709 AGACGACTATGTTAGTGTGTGATG 58.358 41.667 0.00 0.00 39.59 3.07
2169 2209 5.899120 AGACGACTATGTTAGTGTGTGAT 57.101 39.130 0.00 0.00 39.59 3.06
2170 2210 5.700722 AAGACGACTATGTTAGTGTGTGA 57.299 39.130 0.00 0.00 39.59 3.58
2171 2211 5.059343 CGAAAGACGACTATGTTAGTGTGTG 59.941 44.000 0.00 0.00 45.77 3.82
2172 2212 5.152097 CGAAAGACGACTATGTTAGTGTGT 58.848 41.667 0.00 0.00 45.77 3.72
2173 2213 4.030306 GCGAAAGACGACTATGTTAGTGTG 59.970 45.833 0.00 0.00 45.77 3.82
2174 2214 4.082895 AGCGAAAGACGACTATGTTAGTGT 60.083 41.667 0.00 0.00 45.77 3.55
2175 2215 4.263209 CAGCGAAAGACGACTATGTTAGTG 59.737 45.833 0.00 0.00 45.77 2.74
2176 2216 4.413087 CAGCGAAAGACGACTATGTTAGT 58.587 43.478 0.00 0.00 45.77 2.24
2177 2217 3.240861 GCAGCGAAAGACGACTATGTTAG 59.759 47.826 0.00 0.00 45.77 2.34
2178 2218 3.176708 GCAGCGAAAGACGACTATGTTA 58.823 45.455 0.00 0.00 45.77 2.41
2179 2219 1.993370 GCAGCGAAAGACGACTATGTT 59.007 47.619 0.00 0.00 45.77 2.71
2180 2220 1.630148 GCAGCGAAAGACGACTATGT 58.370 50.000 0.00 0.00 45.77 2.29
2181 2221 0.924090 GGCAGCGAAAGACGACTATG 59.076 55.000 0.00 0.00 45.77 2.23
2182 2222 0.525668 CGGCAGCGAAAGACGACTAT 60.526 55.000 0.00 0.00 45.77 2.12
2183 2223 1.154093 CGGCAGCGAAAGACGACTA 60.154 57.895 0.00 0.00 45.77 2.59
2184 2224 2.214181 ATCGGCAGCGAAAGACGACT 62.214 55.000 2.25 0.00 45.77 4.18
2185 2225 1.805945 ATCGGCAGCGAAAGACGAC 60.806 57.895 2.25 0.00 45.77 4.34
2186 2226 1.805539 CATCGGCAGCGAAAGACGA 60.806 57.895 2.69 2.69 45.77 4.20
2187 2227 1.626654 AACATCGGCAGCGAAAGACG 61.627 55.000 0.00 0.00 45.66 4.18
2188 2228 0.179215 CAACATCGGCAGCGAAAGAC 60.179 55.000 0.00 0.00 0.00 3.01
2189 2229 0.602638 ACAACATCGGCAGCGAAAGA 60.603 50.000 0.00 0.00 0.00 2.52
2190 2230 0.238289 AACAACATCGGCAGCGAAAG 59.762 50.000 0.00 0.00 0.00 2.62
2191 2231 0.040514 CAACAACATCGGCAGCGAAA 60.041 50.000 0.00 0.00 0.00 3.46
2192 2232 1.573932 CAACAACATCGGCAGCGAA 59.426 52.632 0.00 0.00 0.00 4.70
2193 2233 2.965147 GCAACAACATCGGCAGCGA 61.965 57.895 0.00 0.00 0.00 4.93
2194 2234 2.502510 GCAACAACATCGGCAGCG 60.503 61.111 0.00 0.00 0.00 5.18
2195 2235 1.443194 CTGCAACAACATCGGCAGC 60.443 57.895 0.00 0.00 46.00 5.25
2196 2236 4.853507 CTGCAACAACATCGGCAG 57.146 55.556 0.00 0.00 46.47 4.85
2197 2237 1.028130 TTTCTGCAACAACATCGGCA 58.972 45.000 0.00 0.00 34.66 5.69
2198 2238 1.001378 AGTTTCTGCAACAACATCGGC 60.001 47.619 9.69 0.00 37.93 5.54
2199 2239 3.044986 CAAGTTTCTGCAACAACATCGG 58.955 45.455 9.69 0.00 37.93 4.18
2200 2240 3.044986 CCAAGTTTCTGCAACAACATCG 58.955 45.455 9.69 0.00 37.93 3.84
2201 2241 4.202050 ACTCCAAGTTTCTGCAACAACATC 60.202 41.667 9.69 0.00 37.93 3.06
2202 2242 3.701040 ACTCCAAGTTTCTGCAACAACAT 59.299 39.130 9.69 0.00 37.93 2.71
2203 2243 3.088532 ACTCCAAGTTTCTGCAACAACA 58.911 40.909 9.69 0.00 37.93 3.33
2204 2244 3.438360 CACTCCAAGTTTCTGCAACAAC 58.562 45.455 0.00 0.00 37.93 3.32
2205 2245 2.426738 CCACTCCAAGTTTCTGCAACAA 59.573 45.455 0.00 0.00 37.93 2.83
2206 2246 2.023673 CCACTCCAAGTTTCTGCAACA 58.976 47.619 0.00 0.00 37.93 3.33
2207 2247 2.033424 GTCCACTCCAAGTTTCTGCAAC 59.967 50.000 0.00 0.00 35.32 4.17
2208 2248 2.297701 GTCCACTCCAAGTTTCTGCAA 58.702 47.619 0.00 0.00 0.00 4.08
2209 2249 1.810031 CGTCCACTCCAAGTTTCTGCA 60.810 52.381 0.00 0.00 0.00 4.41
2210 2250 0.868406 CGTCCACTCCAAGTTTCTGC 59.132 55.000 0.00 0.00 0.00 4.26
2211 2251 1.867233 CACGTCCACTCCAAGTTTCTG 59.133 52.381 0.00 0.00 0.00 3.02
2212 2252 1.202651 CCACGTCCACTCCAAGTTTCT 60.203 52.381 0.00 0.00 0.00 2.52
2213 2253 1.202604 TCCACGTCCACTCCAAGTTTC 60.203 52.381 0.00 0.00 0.00 2.78
2214 2254 0.834612 TCCACGTCCACTCCAAGTTT 59.165 50.000 0.00 0.00 0.00 2.66
2215 2255 0.106149 GTCCACGTCCACTCCAAGTT 59.894 55.000 0.00 0.00 0.00 2.66
2216 2256 1.046472 TGTCCACGTCCACTCCAAGT 61.046 55.000 0.00 0.00 0.00 3.16
2217 2257 0.321671 ATGTCCACGTCCACTCCAAG 59.678 55.000 0.00 0.00 0.00 3.61
2218 2258 1.274167 GTATGTCCACGTCCACTCCAA 59.726 52.381 0.00 0.00 0.00 3.53
2219 2259 0.892755 GTATGTCCACGTCCACTCCA 59.107 55.000 0.00 0.00 0.00 3.86
2220 2260 0.892755 TGTATGTCCACGTCCACTCC 59.107 55.000 0.00 0.00 0.00 3.85
2221 2261 2.165641 TGATGTATGTCCACGTCCACTC 59.834 50.000 0.00 0.00 34.17 3.51
2222 2262 2.176045 TGATGTATGTCCACGTCCACT 58.824 47.619 0.00 0.00 34.17 4.00
2223 2263 2.665649 TGATGTATGTCCACGTCCAC 57.334 50.000 0.00 0.00 34.17 4.02
2224 2264 2.158971 CCATGATGTATGTCCACGTCCA 60.159 50.000 0.00 0.00 34.17 4.02
2225 2265 2.158957 ACCATGATGTATGTCCACGTCC 60.159 50.000 0.00 0.00 34.17 4.79
2226 2266 2.866156 CACCATGATGTATGTCCACGTC 59.134 50.000 0.00 0.00 34.87 4.34
2227 2267 2.499693 TCACCATGATGTATGTCCACGT 59.500 45.455 0.00 0.00 34.87 4.49
2228 2268 2.866156 GTCACCATGATGTATGTCCACG 59.134 50.000 0.00 0.00 34.87 4.94
2229 2269 2.866156 CGTCACCATGATGTATGTCCAC 59.134 50.000 0.00 0.00 34.87 4.02
2230 2270 2.499693 ACGTCACCATGATGTATGTCCA 59.500 45.455 1.81 0.00 44.16 4.02
2231 2271 2.866156 CACGTCACCATGATGTATGTCC 59.134 50.000 3.44 0.00 44.17 4.02
2232 2272 2.866156 CCACGTCACCATGATGTATGTC 59.134 50.000 3.44 0.00 44.17 3.06
2233 2273 2.905075 CCACGTCACCATGATGTATGT 58.095 47.619 3.44 0.00 44.17 2.29
2234 2274 1.599071 GCCACGTCACCATGATGTATG 59.401 52.381 3.44 0.63 44.17 2.39
2235 2275 1.486310 AGCCACGTCACCATGATGTAT 59.514 47.619 3.44 0.00 44.17 2.29
2236 2276 0.901827 AGCCACGTCACCATGATGTA 59.098 50.000 3.44 0.00 44.17 2.29
2237 2277 0.674581 CAGCCACGTCACCATGATGT 60.675 55.000 0.00 0.00 46.70 3.06
2238 2278 1.985447 GCAGCCACGTCACCATGATG 61.985 60.000 0.00 0.00 39.24 3.07
2239 2279 1.746615 GCAGCCACGTCACCATGAT 60.747 57.895 0.00 0.00 0.00 2.45
2240 2280 1.540435 TAGCAGCCACGTCACCATGA 61.540 55.000 0.00 0.00 0.00 3.07
2241 2281 1.079197 TAGCAGCCACGTCACCATG 60.079 57.895 0.00 0.00 0.00 3.66
2242 2282 1.079127 GTAGCAGCCACGTCACCAT 60.079 57.895 0.00 0.00 0.00 3.55
2243 2283 0.896479 TAGTAGCAGCCACGTCACCA 60.896 55.000 0.00 0.00 0.00 4.17
2244 2284 0.458025 GTAGTAGCAGCCACGTCACC 60.458 60.000 0.00 0.00 0.00 4.02
2245 2285 0.797249 CGTAGTAGCAGCCACGTCAC 60.797 60.000 0.00 0.00 0.00 3.67
2246 2286 1.504900 CGTAGTAGCAGCCACGTCA 59.495 57.895 0.00 0.00 0.00 4.35
2247 2287 1.226603 CCGTAGTAGCAGCCACGTC 60.227 63.158 0.00 0.00 32.66 4.34
2248 2288 1.975407 ACCGTAGTAGCAGCCACGT 60.975 57.895 0.00 0.00 32.66 4.49
2249 2289 1.516386 CACCGTAGTAGCAGCCACG 60.516 63.158 0.00 0.00 0.00 4.94
2250 2290 0.460311 ATCACCGTAGTAGCAGCCAC 59.540 55.000 0.00 0.00 0.00 5.01
2251 2291 1.679680 GTATCACCGTAGTAGCAGCCA 59.320 52.381 0.00 0.00 0.00 4.75
2252 2292 1.334779 CGTATCACCGTAGTAGCAGCC 60.335 57.143 0.00 0.00 0.00 4.85
2253 2293 1.332997 ACGTATCACCGTAGTAGCAGC 59.667 52.381 0.00 0.00 39.73 5.25
2254 2294 2.871022 AGACGTATCACCGTAGTAGCAG 59.129 50.000 0.00 0.00 41.98 4.24
2255 2295 2.868583 GAGACGTATCACCGTAGTAGCA 59.131 50.000 5.07 0.00 41.98 3.49
2256 2296 2.222911 GGAGACGTATCACCGTAGTAGC 59.777 54.545 12.92 0.00 41.98 3.58
2257 2297 3.461061 TGGAGACGTATCACCGTAGTAG 58.539 50.000 12.92 0.00 41.98 2.57
2258 2298 3.541996 TGGAGACGTATCACCGTAGTA 57.458 47.619 12.92 0.00 41.98 1.82
2259 2299 2.408271 TGGAGACGTATCACCGTAGT 57.592 50.000 12.92 0.00 41.98 2.73
2260 2300 2.223433 GGTTGGAGACGTATCACCGTAG 60.223 54.545 12.92 0.00 41.98 3.51
2261 2301 1.745087 GGTTGGAGACGTATCACCGTA 59.255 52.381 12.92 0.00 41.98 4.02
2262 2302 0.529378 GGTTGGAGACGTATCACCGT 59.471 55.000 12.92 0.00 45.18 4.83
2263 2303 0.815734 AGGTTGGAGACGTATCACCG 59.184 55.000 12.92 0.00 38.37 4.94
2373 2414 7.689559 GCACTGGGCTCTAGGTTAATAAGTTAT 60.690 40.741 0.00 0.00 40.25 1.89
2441 2486 8.746052 ATTCCGTTTGGACTTCATTTGATATA 57.254 30.769 0.00 0.00 46.45 0.86
2452 2497 8.852135 TCATAAAGTTTTATTCCGTTTGGACTT 58.148 29.630 0.00 0.00 46.45 3.01
2654 2708 4.524802 ATTTTGGTGGATGCCTCTGATA 57.475 40.909 0.00 0.00 0.00 2.15
2696 2750 2.739943 TGGGATCTCACGAGAACAGAT 58.260 47.619 0.00 0.00 41.36 2.90
2772 2826 0.178953 AGGGCAGCAAGGTTGATGTT 60.179 50.000 9.53 0.00 45.71 2.71
2843 2898 8.052141 TCATTGAGAGAGAAGAAGTCATCTAGA 58.948 37.037 0.00 0.00 37.42 2.43
2851 2906 7.479352 TGAAGATCATTGAGAGAGAAGAAGT 57.521 36.000 0.00 0.00 0.00 3.01
2865 2920 9.118300 GAGAAGAACATGGTATTGAAGATCATT 57.882 33.333 0.00 0.00 0.00 2.57
2888 2943 5.067936 GGATAGAACTCCAAGAACATCGAGA 59.932 44.000 0.00 0.00 35.24 4.04
2996 3051 9.017509 TCATGCATAAAAGAGTTCAGAAAAGAT 57.982 29.630 0.00 0.00 0.00 2.40
3059 3114 2.919666 CAATCTAGTTGGCCAAACCG 57.080 50.000 22.47 11.23 43.94 4.44


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

AutoCloner maintained by Alex Coulton.