Multiple sequence alignment - TraesCS2D01G543900

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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 TraesCS2D01G543900 chr2D 100.000 2582 0 0 1 2582 621406254 621403673 0.000000e+00 4769.0
1 TraesCS2D01G543900 chr2D 88.235 136 11 4 1064 1195 528635714 528635848 9.560000e-35 158.0
2 TraesCS2D01G543900 chr2A 87.675 1712 123 45 219 1888 753116995 753115330 0.000000e+00 1912.0
3 TraesCS2D01G543900 chr2A 82.158 695 64 19 1910 2582 753115247 753114591 2.260000e-150 542.0
4 TraesCS2D01G543900 chr2A 88.971 136 10 4 1064 1195 673327382 673327516 2.060000e-36 163.0
5 TraesCS2D01G543900 chr2A 80.870 115 12 4 2166 2279 736311919 736311814 5.920000e-12 82.4
6 TraesCS2D01G543900 chr2A 88.060 67 3 2 12 78 753117259 753117198 9.910000e-10 75.0
7 TraesCS2D01G543900 chr2B 91.104 933 56 13 964 1888 762214321 762213408 0.000000e+00 1238.0
8 TraesCS2D01G543900 chr2B 83.190 928 60 38 12 898 762215316 762214444 0.000000e+00 761.0
9 TraesCS2D01G543900 chr2B 83.598 189 20 5 1936 2121 762207494 762207314 1.590000e-37 167.0
10 TraesCS2D01G543900 chr2B 87.500 136 12 4 1064 1195 627073521 627073655 4.450000e-33 152.0
11 TraesCS2D01G543900 chr2B 86.842 114 10 3 1971 2081 762213289 762213178 3.490000e-24 122.0
12 TraesCS2D01G543900 chr6A 86.466 133 13 4 1066 1194 454712224 454712093 9.630000e-30 141.0
13 TraesCS2D01G543900 chr6A 81.739 115 19 2 2166 2279 584483483 584483370 7.610000e-16 95.3
14 TraesCS2D01G543900 chr6D 85.606 132 16 2 1066 1194 317105970 317105839 4.480000e-28 135.0
15 TraesCS2D01G543900 chr4A 81.667 120 20 2 2166 2285 688423595 688423712 5.880000e-17 99.0
16 TraesCS2D01G543900 chr1B 81.818 121 19 3 2166 2285 72711480 72711598 5.880000e-17 99.0
17 TraesCS2D01G543900 chr6B 81.739 115 19 2 2166 2279 576208581 576208468 7.610000e-16 95.3
18 TraesCS2D01G543900 chr6B 78.322 143 22 3 2185 2318 197228963 197228821 1.650000e-12 84.2


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 TraesCS2D01G543900 chr2D 621403673 621406254 2581 True 4769 4769 100.000000 1 2582 1 chr2D.!!$R1 2581
1 TraesCS2D01G543900 chr2A 753114591 753117259 2668 True 843 1912 85.964333 12 2582 3 chr2A.!!$R2 2570
2 TraesCS2D01G543900 chr2B 762213178 762215316 2138 True 707 1238 87.045333 12 2081 3 chr2B.!!$R2 2069

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
806 909 0.037303 CCTTCACACCATCACAGCCT 59.963 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1930 0.02811 GGCGCAAATCTCCGTCAATC 59.972 55.0 10.83 0.0 0.0 2.67 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
52 55 6.371825 GGAGTACCGTTTGATTTGAATCTTCT 59.628 38.462 5.42 0.00 36.39 2.85
57 60 5.455392 CGTTTGATTTGAATCTTCTGTGCT 58.545 37.500 5.42 0.00 36.39 4.40
58 61 5.916883 CGTTTGATTTGAATCTTCTGTGCTT 59.083 36.000 5.42 0.00 36.39 3.91
59 62 6.418819 CGTTTGATTTGAATCTTCTGTGCTTT 59.581 34.615 5.42 0.00 36.39 3.51
60 63 7.357859 CGTTTGATTTGAATCTTCTGTGCTTTC 60.358 37.037 5.42 0.00 36.39 2.62
61 64 5.692814 TGATTTGAATCTTCTGTGCTTTCG 58.307 37.500 5.42 0.00 36.39 3.46
62 65 4.488126 TTTGAATCTTCTGTGCTTTCGG 57.512 40.909 0.00 0.00 0.00 4.30
79 82 2.280797 GCGCCACAGTGGAACAGA 60.281 61.111 24.96 0.00 40.96 3.41
81 93 1.961277 CGCCACAGTGGAACAGACC 60.961 63.158 24.96 2.25 40.96 3.85
82 94 1.148273 GCCACAGTGGAACAGACCA 59.852 57.895 24.96 0.00 40.96 4.02
88 100 3.544772 TGGAACAGACCACTCGCA 58.455 55.556 0.00 0.00 34.77 5.10
89 101 2.057830 TGGAACAGACCACTCGCAT 58.942 52.632 0.00 0.00 34.77 4.73
90 102 1.262417 TGGAACAGACCACTCGCATA 58.738 50.000 0.00 0.00 34.77 3.14
125 156 0.684479 TGATGAGCCGAGGCAGTAGT 60.684 55.000 17.18 0.00 44.88 2.73
126 157 0.461961 GATGAGCCGAGGCAGTAGTT 59.538 55.000 17.18 0.00 44.88 2.24
129 160 2.108168 TGAGCCGAGGCAGTAGTTTAT 58.892 47.619 17.18 0.00 44.88 1.40
131 162 3.702548 TGAGCCGAGGCAGTAGTTTATTA 59.297 43.478 17.18 0.00 44.88 0.98
132 163 4.202121 TGAGCCGAGGCAGTAGTTTATTAG 60.202 45.833 17.18 0.00 44.88 1.73
133 164 3.705072 AGCCGAGGCAGTAGTTTATTAGT 59.295 43.478 17.18 0.00 44.88 2.24
134 165 4.891756 AGCCGAGGCAGTAGTTTATTAGTA 59.108 41.667 17.18 0.00 44.88 1.82
135 166 4.981054 GCCGAGGCAGTAGTTTATTAGTAC 59.019 45.833 9.58 0.00 41.49 2.73
139 170 6.238320 CGAGGCAGTAGTTTATTAGTACGACT 60.238 42.308 0.00 0.00 37.67 4.18
141 172 5.975939 GGCAGTAGTTTATTAGTACGACTGG 59.024 44.000 14.31 1.38 43.67 4.00
183 239 6.015180 ACGGCTGGGATTCGTAATTTACTATA 60.015 38.462 0.00 0.00 35.23 1.31
185 241 7.384477 GGCTGGGATTCGTAATTTACTATACT 58.616 38.462 5.11 0.00 0.00 2.12
189 245 6.309737 GGGATTCGTAATTTACTATACTGCCG 59.690 42.308 5.11 0.00 0.00 5.69
190 246 7.086376 GGATTCGTAATTTACTATACTGCCGA 58.914 38.462 5.11 0.00 0.00 5.54
194 250 5.682862 CGTAATTTACTATACTGCCGAACGT 59.317 40.000 5.11 0.00 0.00 3.99
196 252 4.970662 TTTACTATACTGCCGAACGTCT 57.029 40.909 0.00 0.00 0.00 4.18
204 260 2.478894 ACTGCCGAACGTCTGTAATTTG 59.521 45.455 0.00 0.00 0.00 2.32
214 270 0.732571 CTGTAATTTGCACCGCCGAT 59.267 50.000 0.00 0.00 0.00 4.18
215 271 1.937223 CTGTAATTTGCACCGCCGATA 59.063 47.619 0.00 0.00 0.00 2.92
216 272 2.548057 CTGTAATTTGCACCGCCGATAT 59.452 45.455 0.00 0.00 0.00 1.63
217 273 3.729966 TGTAATTTGCACCGCCGATATA 58.270 40.909 0.00 0.00 0.00 0.86
226 314 4.158384 GCACCGCCGATATATTCAATTTG 58.842 43.478 0.00 0.00 0.00 2.32
234 322 5.473162 CCGATATATTCAATTTGGTCAGGCA 59.527 40.000 0.00 0.00 0.00 4.75
361 449 0.179171 CTACCCAGCGTCACGTACTG 60.179 60.000 0.00 0.00 0.00 2.74
362 450 0.606130 TACCCAGCGTCACGTACTGA 60.606 55.000 6.41 0.00 33.10 3.41
460 553 1.278413 TCCGATCCGATCCGATCTAGT 59.722 52.381 18.10 0.00 37.16 2.57
461 554 1.666700 CCGATCCGATCCGATCTAGTC 59.333 57.143 18.10 1.38 37.16 2.59
464 557 4.182339 CGATCCGATCCGATCTAGTCTAA 58.818 47.826 18.10 0.00 37.16 2.10
623 720 0.963962 AGTAAACTCGGCGAAGACCA 59.036 50.000 12.13 0.00 0.00 4.02
639 736 1.908793 CCAGTCTCGTGTGGGAGGT 60.909 63.158 0.00 0.00 34.74 3.85
653 750 0.632294 GGAGGTAGGGAGAGTGAGGT 59.368 60.000 0.00 0.00 0.00 3.85
654 751 1.007359 GGAGGTAGGGAGAGTGAGGTT 59.993 57.143 0.00 0.00 0.00 3.50
806 909 0.037303 CCTTCACACCATCACAGCCT 59.963 55.000 0.00 0.00 0.00 4.58
807 910 1.546323 CCTTCACACCATCACAGCCTT 60.546 52.381 0.00 0.00 0.00 4.35
809 912 1.059098 TCACACCATCACAGCCTTCT 58.941 50.000 0.00 0.00 0.00 2.85
810 913 1.421268 TCACACCATCACAGCCTTCTT 59.579 47.619 0.00 0.00 0.00 2.52
817 926 4.394712 ACAGCCTTCTTCCCGCCG 62.395 66.667 0.00 0.00 0.00 6.46
822 931 3.775654 CTTCTTCCCGCCGCCTCT 61.776 66.667 0.00 0.00 0.00 3.69
831 940 4.527583 GCCGCCTCTCAGCTCCAG 62.528 72.222 0.00 0.00 0.00 3.86
835 944 2.583520 CCTCTCAGCTCCAGCACC 59.416 66.667 0.48 0.00 45.16 5.01
855 964 3.228017 GGCTCGGCTCCCTCTACC 61.228 72.222 0.00 0.00 0.00 3.18
861 970 3.544772 GCTCCCTCTACCCAGAGC 58.455 66.667 0.00 0.00 46.08 4.09
865 974 0.118346 TCCCTCTACCCAGAGCCAAA 59.882 55.000 0.00 0.00 46.08 3.28
866 975 0.543749 CCCTCTACCCAGAGCCAAAG 59.456 60.000 0.00 0.00 46.08 2.77
868 977 1.909302 CCTCTACCCAGAGCCAAAGAA 59.091 52.381 0.00 0.00 46.08 2.52
874 983 2.097825 CCCAGAGCCAAAGAATCAAGG 58.902 52.381 0.00 0.00 0.00 3.61
881 990 3.062042 GCCAAAGAATCAAGGCTGTTTG 58.938 45.455 0.00 0.00 43.70 2.93
888 997 1.229428 TCAAGGCTGTTTGAAGCTCG 58.771 50.000 0.00 0.00 43.06 5.03
902 1041 2.577112 CTCGAGATCACGCGCGTT 60.577 61.111 35.90 21.63 39.03 4.84
903 1042 2.126618 TCGAGATCACGCGCGTTT 60.127 55.556 35.90 24.20 39.03 3.60
906 1045 1.742900 CGAGATCACGCGCGTTTCAT 61.743 55.000 35.90 24.65 32.29 2.57
907 1046 0.370273 GAGATCACGCGCGTTTCATT 59.630 50.000 35.90 17.97 0.00 2.57
908 1047 0.370273 AGATCACGCGCGTTTCATTC 59.630 50.000 35.90 23.23 0.00 2.67
909 1048 0.094558 GATCACGCGCGTTTCATTCA 59.905 50.000 35.90 11.31 0.00 2.57
911 1050 2.139811 CACGCGCGTTTCATTCAGC 61.140 57.895 35.90 0.00 0.00 4.26
912 1051 2.574212 CGCGCGTTTCATTCAGCC 60.574 61.111 24.19 0.00 0.00 4.85
914 1053 2.485122 CGCGTTTCATTCAGCCCC 59.515 61.111 0.00 0.00 0.00 5.80
915 1054 2.040544 CGCGTTTCATTCAGCCCCT 61.041 57.895 0.00 0.00 0.00 4.79
916 1055 1.803289 GCGTTTCATTCAGCCCCTC 59.197 57.895 0.00 0.00 0.00 4.30
917 1056 0.678048 GCGTTTCATTCAGCCCCTCT 60.678 55.000 0.00 0.00 0.00 3.69
918 1057 1.089920 CGTTTCATTCAGCCCCTCTG 58.910 55.000 0.00 0.00 44.21 3.35
919 1058 1.467920 GTTTCATTCAGCCCCTCTGG 58.532 55.000 0.00 0.00 43.06 3.86
920 1059 1.075601 TTTCATTCAGCCCCTCTGGT 58.924 50.000 0.00 0.00 43.06 4.00
923 1062 1.542375 ATTCAGCCCCTCTGGTGGT 60.542 57.895 0.00 0.00 43.06 4.16
924 1063 1.856539 ATTCAGCCCCTCTGGTGGTG 61.857 60.000 0.00 0.00 43.06 4.17
925 1064 4.039092 CAGCCCCTCTGGTGGTGG 62.039 72.222 0.00 0.00 39.15 4.61
936 1089 4.778143 GTGGTGGTAGCCAGGCCG 62.778 72.222 8.22 0.00 39.53 6.13
939 1092 3.075005 GTGGTAGCCAGGCCGAGA 61.075 66.667 8.22 0.00 32.34 4.04
940 1093 3.075005 TGGTAGCCAGGCCGAGAC 61.075 66.667 8.22 0.96 0.00 3.36
941 1094 3.075005 GGTAGCCAGGCCGAGACA 61.075 66.667 8.22 0.00 0.00 3.41
945 1098 2.781431 TAGCCAGGCCGAGACAGTCA 62.781 60.000 8.22 0.00 0.00 3.41
947 1100 2.262915 CAGGCCGAGACAGTCACC 59.737 66.667 2.66 0.00 0.00 4.02
949 1102 4.436998 GGCCGAGACAGTCACCGG 62.437 72.222 22.85 22.85 44.34 5.28
957 1110 4.760047 CAGTCACCGGGCGGAAGG 62.760 72.222 6.32 0.00 38.96 3.46
976 1141 1.893919 GAGCGGAAGGACTGAAGCCT 61.894 60.000 0.00 0.00 37.35 4.58
1230 1395 2.193536 GCTCGCCACCACCAACTTT 61.194 57.895 0.00 0.00 0.00 2.66
1241 1406 1.076727 CCAACTTTCCCCAGGACCC 59.923 63.158 0.00 0.00 0.00 4.46
1347 1512 4.392166 TCCTACAGCGGGCCCAGA 62.392 66.667 24.92 3.02 0.00 3.86
1569 1734 2.573869 GAGCTGTGCACCGAGCTA 59.426 61.111 26.43 1.98 45.72 3.32
1664 1835 9.640952 TTTTTCTTCTATTCTTTTTCCTCCTGA 57.359 29.630 0.00 0.00 0.00 3.86
1665 1836 9.813826 TTTTCTTCTATTCTTTTTCCTCCTGAT 57.186 29.630 0.00 0.00 0.00 2.90
1666 1837 9.813826 TTTCTTCTATTCTTTTTCCTCCTGATT 57.186 29.630 0.00 0.00 0.00 2.57
1753 1929 4.351192 GCGATAAGAATTGCGGTTGATTT 58.649 39.130 0.00 0.00 32.83 2.17
1754 1930 4.204978 GCGATAAGAATTGCGGTTGATTTG 59.795 41.667 0.00 0.00 32.83 2.32
1755 1931 5.568482 CGATAAGAATTGCGGTTGATTTGA 58.432 37.500 0.00 0.00 0.00 2.69
1757 1933 6.692681 CGATAAGAATTGCGGTTGATTTGATT 59.307 34.615 0.00 0.00 0.00 2.57
1758 1934 7.305590 CGATAAGAATTGCGGTTGATTTGATTG 60.306 37.037 0.00 0.00 0.00 2.67
1759 1935 5.389859 AGAATTGCGGTTGATTTGATTGA 57.610 34.783 0.00 0.00 0.00 2.57
1760 1936 5.163513 AGAATTGCGGTTGATTTGATTGAC 58.836 37.500 0.00 0.00 0.00 3.18
1761 1937 2.610219 TGCGGTTGATTTGATTGACG 57.390 45.000 0.00 0.00 0.00 4.35
1762 1938 1.198867 TGCGGTTGATTTGATTGACGG 59.801 47.619 0.00 0.00 0.00 4.79
1763 1939 1.466950 GCGGTTGATTTGATTGACGGA 59.533 47.619 0.00 0.00 0.00 4.69
1764 1940 2.476185 GCGGTTGATTTGATTGACGGAG 60.476 50.000 0.00 0.00 0.00 4.63
1765 1941 3.000041 CGGTTGATTTGATTGACGGAGA 59.000 45.455 0.00 0.00 0.00 3.71
1766 1942 3.623060 CGGTTGATTTGATTGACGGAGAT 59.377 43.478 0.00 0.00 0.00 2.75
1767 1943 4.094887 CGGTTGATTTGATTGACGGAGATT 59.905 41.667 0.00 0.00 0.00 2.40
1768 1944 5.391950 CGGTTGATTTGATTGACGGAGATTT 60.392 40.000 0.00 0.00 0.00 2.17
1769 1945 5.801947 GGTTGATTTGATTGACGGAGATTTG 59.198 40.000 0.00 0.00 0.00 2.32
1770 1946 4.985413 TGATTTGATTGACGGAGATTTGC 58.015 39.130 0.00 0.00 0.00 3.68
1858 2042 0.040425 CTTGCGTGCAAGTGTAACCC 60.040 55.000 23.06 0.00 45.91 4.11
1881 2065 2.101917 AGAGCATTTGCAGCAACTTTGT 59.898 40.909 7.54 0.00 45.16 2.83
1888 2072 3.523606 TGCAGCAACTTTGTGAATTGT 57.476 38.095 0.00 0.00 0.00 2.71
1889 2073 3.859443 TGCAGCAACTTTGTGAATTGTT 58.141 36.364 0.00 0.00 0.00 2.83
1904 2127 4.100189 TGAATTGTTTAGTGGTGGGGTTTG 59.900 41.667 0.00 0.00 0.00 2.93
1905 2128 3.383698 TTGTTTAGTGGTGGGGTTTGA 57.616 42.857 0.00 0.00 0.00 2.69
1906 2129 2.938838 TGTTTAGTGGTGGGGTTTGAG 58.061 47.619 0.00 0.00 0.00 3.02
1907 2130 2.510382 TGTTTAGTGGTGGGGTTTGAGA 59.490 45.455 0.00 0.00 0.00 3.27
1908 2131 3.139397 TGTTTAGTGGTGGGGTTTGAGAT 59.861 43.478 0.00 0.00 0.00 2.75
1909 2132 3.433306 TTAGTGGTGGGGTTTGAGATG 57.567 47.619 0.00 0.00 0.00 2.90
1910 2133 1.149101 AGTGGTGGGGTTTGAGATGT 58.851 50.000 0.00 0.00 0.00 3.06
1912 2135 1.886542 GTGGTGGGGTTTGAGATGTTC 59.113 52.381 0.00 0.00 0.00 3.18
1947 2196 2.767496 CTCCCTCCCTCCCTGCTG 60.767 72.222 0.00 0.00 0.00 4.41
1958 2207 2.303022 CCTCCCTGCTGTTTCTTCTGTA 59.697 50.000 0.00 0.00 0.00 2.74
1959 2208 3.330267 CTCCCTGCTGTTTCTTCTGTAC 58.670 50.000 0.00 0.00 0.00 2.90
1963 2212 5.248477 TCCCTGCTGTTTCTTCTGTACTATT 59.752 40.000 0.00 0.00 0.00 1.73
2017 2269 6.655003 TGTATTCAAACTGGACTGAAGATTCC 59.345 38.462 0.00 0.00 35.14 3.01
2025 2277 3.072915 TGGACTGAAGATTCCTCTTTGCA 59.927 43.478 0.00 0.00 41.87 4.08
2096 2351 6.327934 CAATTTGAAGAAGATGGTGGATCAC 58.672 40.000 0.00 0.00 32.86 3.06
2111 2366 1.535462 GATCACGTTCTGGGTTTGTGG 59.465 52.381 0.00 0.00 0.00 4.17
2115 2370 0.306533 CGTTCTGGGTTTGTGGTTCG 59.693 55.000 0.00 0.00 0.00 3.95
2117 2372 1.064952 GTTCTGGGTTTGTGGTTCGTG 59.935 52.381 0.00 0.00 0.00 4.35
2126 2381 4.500716 GGTTTGTGGTTCGTGGATTTTGAT 60.501 41.667 0.00 0.00 0.00 2.57
2132 2387 4.215399 TGGTTCGTGGATTTTGATGAGTTC 59.785 41.667 0.00 0.00 0.00 3.01
2133 2388 4.394795 GTTCGTGGATTTTGATGAGTTCG 58.605 43.478 0.00 0.00 0.00 3.95
2145 2400 1.006825 TGAGTTCGATGGCGTGTTCG 61.007 55.000 0.00 0.00 38.98 3.95
2160 2415 0.655733 GTTCGCGGATAACATGTGGG 59.344 55.000 6.13 0.00 0.00 4.61
2164 2419 1.810031 CGCGGATAACATGTGGGTGAT 60.810 52.381 0.00 0.00 0.00 3.06
2198 2454 4.838486 GCGTCGAGCTCGGGTGAG 62.838 72.222 33.98 20.85 45.49 3.51
2211 2467 2.076863 CGGGTGAGAAGGTGATTTGTC 58.923 52.381 0.00 0.00 0.00 3.18
2212 2468 2.549992 CGGGTGAGAAGGTGATTTGTCA 60.550 50.000 0.00 0.00 0.00 3.58
2222 2478 9.912634 GAGAAGGTGATTTGTCATTTTTATTCA 57.087 29.630 0.00 0.00 0.00 2.57
2230 2486 9.925268 GATTTGTCATTTTTATTCATTGATGGC 57.075 29.630 0.00 0.00 0.00 4.40
2231 2487 9.675464 ATTTGTCATTTTTATTCATTGATGGCT 57.325 25.926 0.00 0.00 0.00 4.75
2232 2488 9.504708 TTTGTCATTTTTATTCATTGATGGCTT 57.495 25.926 0.00 0.00 0.00 4.35
2241 2497 3.349927 TCATTGATGGCTTCTCTGGTTG 58.650 45.455 1.86 0.00 0.00 3.77
2254 2510 0.673644 CTGGTTGTGCCGGAGTTAGG 60.674 60.000 5.05 0.00 46.81 2.69
2259 2515 1.116536 TGTGCCGGAGTTAGGTGACA 61.117 55.000 5.05 0.00 0.00 3.58
2267 2523 3.364964 CGGAGTTAGGTGACAAATGTTGC 60.365 47.826 0.00 0.00 0.00 4.17
2293 2549 7.143340 TGACAAGCTCAAAAGATTCTTCATTG 58.857 34.615 0.00 2.24 0.00 2.82
2408 2674 7.448161 TCTTCGGGATATAAAAGGACACGTATA 59.552 37.037 0.00 0.00 0.00 1.47
2409 2675 7.707624 TCGGGATATAAAAGGACACGTATAT 57.292 36.000 0.00 0.00 0.00 0.86
2410 2676 7.765307 TCGGGATATAAAAGGACACGTATATC 58.235 38.462 0.00 0.00 36.12 1.63
2411 2677 7.394077 TCGGGATATAAAAGGACACGTATATCA 59.606 37.037 11.02 0.00 37.54 2.15
2412 2678 7.487189 CGGGATATAAAAGGACACGTATATCAC 59.513 40.741 11.02 7.58 37.54 3.06
2413 2679 7.763071 GGGATATAAAAGGACACGTATATCACC 59.237 40.741 11.02 7.33 37.54 4.02
2414 2680 8.308931 GGATATAAAAGGACACGTATATCACCA 58.691 37.037 11.02 0.00 37.54 4.17
2415 2681 9.871238 GATATAAAAGGACACGTATATCACCAT 57.129 33.333 6.03 0.00 36.55 3.55
2421 2687 8.433421 AAGGACACGTATATCACCATAAAAAG 57.567 34.615 0.00 0.00 0.00 2.27
2438 2704 7.387948 CCATAAAAAGAACACTACTACACTGCT 59.612 37.037 0.00 0.00 0.00 4.24
2439 2705 9.419297 CATAAAAAGAACACTACTACACTGCTA 57.581 33.333 0.00 0.00 0.00 3.49
2440 2706 7.710766 AAAAAGAACACTACTACACTGCTAC 57.289 36.000 0.00 0.00 0.00 3.58
2441 2707 6.401047 AAAGAACACTACTACACTGCTACA 57.599 37.500 0.00 0.00 0.00 2.74
2442 2708 5.630661 AGAACACTACTACACTGCTACAG 57.369 43.478 0.00 0.00 37.52 2.74
2443 2709 5.071370 AGAACACTACTACACTGCTACAGT 58.929 41.667 0.00 0.00 46.51 3.55
2444 2710 5.181622 AGAACACTACTACACTGCTACAGTC 59.818 44.000 0.00 0.00 43.43 3.51
2445 2711 4.395625 ACACTACTACACTGCTACAGTCA 58.604 43.478 0.00 0.00 43.43 3.41
2446 2712 4.456222 ACACTACTACACTGCTACAGTCAG 59.544 45.833 0.00 1.32 43.43 3.51
2447 2713 4.456222 CACTACTACACTGCTACAGTCAGT 59.544 45.833 13.24 13.24 43.43 3.41
2448 2714 5.642491 CACTACTACACTGCTACAGTCAGTA 59.358 44.000 13.82 13.82 43.43 2.74
2449 2715 6.148976 CACTACTACACTGCTACAGTCAGTAA 59.851 42.308 14.76 5.14 43.43 2.24
2450 2716 5.373981 ACTACACTGCTACAGTCAGTAAC 57.626 43.478 8.89 0.00 43.43 2.50
2451 2717 3.284323 ACACTGCTACAGTCAGTAACG 57.716 47.619 0.00 0.00 43.43 3.18
2452 2718 2.882761 ACACTGCTACAGTCAGTAACGA 59.117 45.455 0.00 0.00 43.43 3.85
2453 2719 3.058155 ACACTGCTACAGTCAGTAACGAG 60.058 47.826 0.00 0.00 43.43 4.18
2454 2720 3.188667 CACTGCTACAGTCAGTAACGAGA 59.811 47.826 0.00 0.00 43.43 4.04
2455 2721 4.011023 ACTGCTACAGTCAGTAACGAGAT 58.989 43.478 0.00 0.00 41.21 2.75
2456 2722 5.064834 CACTGCTACAGTCAGTAACGAGATA 59.935 44.000 0.00 0.00 43.43 1.98
2457 2723 5.646793 ACTGCTACAGTCAGTAACGAGATAA 59.353 40.000 0.00 0.00 41.21 1.75
2458 2724 6.150641 ACTGCTACAGTCAGTAACGAGATAAA 59.849 38.462 0.00 0.00 41.21 1.40
2459 2725 7.096884 TGCTACAGTCAGTAACGAGATAAAT 57.903 36.000 0.00 0.00 30.92 1.40
2460 2726 8.217131 TGCTACAGTCAGTAACGAGATAAATA 57.783 34.615 0.00 0.00 30.92 1.40
2461 2727 8.127327 TGCTACAGTCAGTAACGAGATAAATAC 58.873 37.037 0.00 0.00 30.92 1.89
2484 2750 3.230608 TGGCCCACCAATTTGAACA 57.769 47.368 0.00 0.00 45.37 3.18
2529 2795 6.381498 TCCTCCAAACCACATTACTTATCA 57.619 37.500 0.00 0.00 0.00 2.15
2540 2806 9.959721 ACCACATTACTTATCACTGATTTAGTT 57.040 29.630 10.21 0.00 37.60 2.24
2549 2815 9.234384 CTTATCACTGATTTAGTTGTAGTACCG 57.766 37.037 0.00 0.00 37.60 4.02
2550 2816 6.822667 TCACTGATTTAGTTGTAGTACCGA 57.177 37.500 0.00 0.00 37.60 4.69
2551 2817 7.400599 TCACTGATTTAGTTGTAGTACCGAT 57.599 36.000 0.00 0.00 37.60 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.699225 CCGCTAGGATATGCACGGCAT 62.699 57.143 14.43 14.43 45.89 4.40
8 9 1.006220 CGCTAGGATATGCACGGCA 60.006 57.895 0.00 1.01 44.86 5.69
9 10 1.738099 CCGCTAGGATATGCACGGC 60.738 63.158 9.68 3.88 41.02 5.68
10 11 1.079819 CCCGCTAGGATATGCACGG 60.080 63.158 13.86 13.86 41.02 4.94
57 60 3.758973 TTCCACTGTGGCGCCGAAA 62.759 57.895 23.90 8.79 37.47 3.46
58 61 4.243008 TTCCACTGTGGCGCCGAA 62.243 61.111 23.90 15.03 37.47 4.30
59 62 4.980805 GTTCCACTGTGGCGCCGA 62.981 66.667 23.90 10.19 37.47 5.54
61 64 3.357079 CTGTTCCACTGTGGCGCC 61.357 66.667 22.73 22.73 37.47 6.53
62 65 2.280797 TCTGTTCCACTGTGGCGC 60.281 61.111 22.02 16.08 37.47 6.53
79 82 2.665649 TCGTGAATTATGCGAGTGGT 57.334 45.000 0.00 0.00 0.00 4.16
81 93 6.986424 TTACTATCGTGAATTATGCGAGTG 57.014 37.500 0.00 3.43 38.06 3.51
82 94 7.865889 TCATTTACTATCGTGAATTATGCGAGT 59.134 33.333 0.00 0.00 38.06 4.18
83 95 8.227731 TCATTTACTATCGTGAATTATGCGAG 57.772 34.615 0.00 0.00 38.06 5.03
84 96 8.647226 CATCATTTACTATCGTGAATTATGCGA 58.353 33.333 0.00 1.86 39.02 5.10
85 97 8.647226 TCATCATTTACTATCGTGAATTATGCG 58.353 33.333 4.91 0.00 33.86 4.73
88 100 9.155975 GGCTCATCATTTACTATCGTGAATTAT 57.844 33.333 0.00 0.00 27.98 1.28
89 101 7.328493 CGGCTCATCATTTACTATCGTGAATTA 59.672 37.037 0.00 0.00 27.98 1.40
90 102 6.146184 CGGCTCATCATTTACTATCGTGAATT 59.854 38.462 0.00 0.00 27.98 2.17
112 143 4.056092 ACTAATAAACTACTGCCTCGGC 57.944 45.455 0.00 0.00 42.35 5.54
117 148 5.975939 CCAGTCGTACTAATAAACTACTGCC 59.024 44.000 0.00 0.00 37.82 4.85
125 156 3.106054 TGGGGCCAGTCGTACTAATAAA 58.894 45.455 4.39 0.00 0.00 1.40
126 157 2.749600 TGGGGCCAGTCGTACTAATAA 58.250 47.619 4.39 0.00 0.00 1.40
129 160 0.609662 GTTGGGGCCAGTCGTACTAA 59.390 55.000 4.39 0.00 0.00 2.24
131 162 1.412453 TTGTTGGGGCCAGTCGTACT 61.412 55.000 4.39 0.00 0.00 2.73
132 163 0.535553 TTTGTTGGGGCCAGTCGTAC 60.536 55.000 4.39 0.00 0.00 3.67
133 164 0.183014 TTTTGTTGGGGCCAGTCGTA 59.817 50.000 4.39 0.00 0.00 3.43
134 165 1.076632 TTTTGTTGGGGCCAGTCGT 60.077 52.632 4.39 0.00 0.00 4.34
135 166 1.362355 GTTTTGTTGGGGCCAGTCG 59.638 57.895 4.39 0.00 0.00 4.18
139 170 2.759973 TGCGTTTTGTTGGGGCCA 60.760 55.556 4.39 0.00 0.00 5.36
141 172 1.299850 GTCTGCGTTTTGTTGGGGC 60.300 57.895 0.00 0.00 0.00 5.80
183 239 2.450609 AATTACAGACGTTCGGCAGT 57.549 45.000 0.00 0.70 0.00 4.40
185 241 1.195900 GCAAATTACAGACGTTCGGCA 59.804 47.619 0.00 0.00 0.00 5.69
189 245 2.834689 CGGTGCAAATTACAGACGTTC 58.165 47.619 0.00 0.00 0.00 3.95
190 246 1.069500 GCGGTGCAAATTACAGACGTT 60.069 47.619 0.00 0.00 0.00 3.99
194 250 0.320858 TCGGCGGTGCAAATTACAGA 60.321 50.000 7.21 0.00 0.00 3.41
196 252 2.025589 TATCGGCGGTGCAAATTACA 57.974 45.000 7.21 0.00 0.00 2.41
204 260 4.158384 CAAATTGAATATATCGGCGGTGC 58.842 43.478 7.21 0.00 0.00 5.01
214 270 5.048782 GCGATGCCTGACCAAATTGAATATA 60.049 40.000 0.00 0.00 0.00 0.86
215 271 4.261741 GCGATGCCTGACCAAATTGAATAT 60.262 41.667 0.00 0.00 0.00 1.28
216 272 3.066621 GCGATGCCTGACCAAATTGAATA 59.933 43.478 0.00 0.00 0.00 1.75
217 273 2.159198 GCGATGCCTGACCAAATTGAAT 60.159 45.455 0.00 0.00 0.00 2.57
234 322 2.573869 CTCACTGTCACGGGCGAT 59.426 61.111 0.00 0.00 0.00 4.58
307 395 2.243736 GGTAGGGTTGGATTGGATTGGA 59.756 50.000 0.00 0.00 0.00 3.53
340 428 2.703798 TACGTGACGCTGGGTAGGC 61.704 63.158 4.25 0.00 0.00 3.93
341 429 1.138247 GTACGTGACGCTGGGTAGG 59.862 63.158 4.25 0.00 0.00 3.18
440 528 1.278413 ACTAGATCGGATCGGATCGGA 59.722 52.381 27.79 24.59 45.90 4.55
460 553 0.466739 TCCGGCCGCACTAGATTAGA 60.467 55.000 22.85 4.17 0.00 2.10
461 554 0.039074 CTCCGGCCGCACTAGATTAG 60.039 60.000 22.85 1.22 0.00 1.73
464 557 3.917760 GCTCCGGCCGCACTAGAT 61.918 66.667 22.85 0.00 0.00 1.98
560 657 2.417586 GGGATAACACGTTTCCTTTCGG 59.582 50.000 0.00 0.00 0.00 4.30
562 659 3.119955 GCAGGGATAACACGTTTCCTTTC 60.120 47.826 0.00 0.00 0.00 2.62
623 720 0.323542 CCTACCTCCCACACGAGACT 60.324 60.000 0.00 0.00 30.97 3.24
639 736 2.559931 CCCTTCAACCTCACTCTCCCTA 60.560 54.545 0.00 0.00 0.00 3.53
653 750 1.228124 CACCTTCCGCACCCTTCAA 60.228 57.895 0.00 0.00 0.00 2.69
654 751 2.429930 CACCTTCCGCACCCTTCA 59.570 61.111 0.00 0.00 0.00 3.02
806 909 3.771160 GAGAGGCGGCGGGAAGAA 61.771 66.667 9.78 0.00 0.00 2.52
817 926 2.125188 GTGCTGGAGCTGAGAGGC 60.125 66.667 0.00 0.00 42.66 4.70
818 927 2.583520 GGTGCTGGAGCTGAGAGG 59.416 66.667 0.00 0.00 42.66 3.69
841 950 2.279073 CTGGGTAGAGGGAGCCGA 59.721 66.667 0.00 0.00 40.03 5.54
842 951 1.830408 CTCTGGGTAGAGGGAGCCG 60.830 68.421 0.00 0.00 45.47 5.52
853 962 2.556114 CCTTGATTCTTTGGCTCTGGGT 60.556 50.000 0.00 0.00 0.00 4.51
855 964 1.475682 GCCTTGATTCTTTGGCTCTGG 59.524 52.381 0.00 0.00 41.92 3.86
861 970 4.589216 TCAAACAGCCTTGATTCTTTGG 57.411 40.909 0.00 0.00 30.31 3.28
865 974 3.494332 AGCTTCAAACAGCCTTGATTCT 58.506 40.909 0.00 0.00 41.12 2.40
866 975 3.669023 CGAGCTTCAAACAGCCTTGATTC 60.669 47.826 0.00 0.00 41.12 2.52
868 977 1.808945 CGAGCTTCAAACAGCCTTGAT 59.191 47.619 0.00 0.00 41.12 2.57
874 983 2.093467 GTGATCTCGAGCTTCAAACAGC 59.907 50.000 16.40 4.10 40.44 4.40
877 986 1.059835 GCGTGATCTCGAGCTTCAAAC 59.940 52.381 20.54 9.84 0.00 2.93
879 988 0.798389 CGCGTGATCTCGAGCTTCAA 60.798 55.000 20.54 0.00 0.00 2.69
881 990 3.594762 CGCGTGATCTCGAGCTTC 58.405 61.111 20.54 7.88 0.00 3.86
888 997 0.370273 AATGAAACGCGCGTGATCTC 59.630 50.000 38.44 27.68 0.00 2.75
908 1047 4.039092 CCACCACCAGAGGGGCTG 62.039 72.222 0.00 0.00 44.49 4.85
909 1048 3.188355 TACCACCACCAGAGGGGCT 62.188 63.158 0.00 0.00 42.05 5.19
911 1050 2.670148 GCTACCACCACCAGAGGGG 61.670 68.421 0.00 0.00 44.81 4.79
912 1051 2.670148 GGCTACCACCACCAGAGGG 61.670 68.421 0.00 0.00 41.29 4.30
914 1053 3.805928 TGGCTACCACCACCAGAG 58.194 61.111 0.00 0.00 33.75 3.35
917 1056 3.646715 GCCTGGCTACCACCACCA 61.647 66.667 12.43 0.00 35.33 4.17
918 1057 4.426313 GGCCTGGCTACCACCACC 62.426 72.222 19.68 0.00 35.33 4.61
919 1058 4.778143 CGGCCTGGCTACCACCAC 62.778 72.222 19.68 0.00 35.33 4.16
923 1062 3.075005 GTCTCGGCCTGGCTACCA 61.075 66.667 19.68 0.00 0.00 3.25
924 1063 3.075005 TGTCTCGGCCTGGCTACC 61.075 66.667 19.68 0.41 0.00 3.18
925 1064 2.286127 GACTGTCTCGGCCTGGCTAC 62.286 65.000 19.68 12.07 0.00 3.58
936 1089 4.436998 CCGCCCGGTGACTGTCTC 62.437 72.222 9.51 5.31 0.00 3.36
937 1090 4.988716 TCCGCCCGGTGACTGTCT 62.989 66.667 9.51 0.00 36.47 3.41
939 1092 4.003788 CTTCCGCCCGGTGACTGT 62.004 66.667 6.61 0.00 36.47 3.55
940 1093 4.760047 CCTTCCGCCCGGTGACTG 62.760 72.222 6.61 0.00 36.47 3.51
949 1102 4.840005 CCTTCCGCTCCTTCCGCC 62.840 72.222 0.00 0.00 0.00 6.13
957 1110 1.448717 GGCTTCAGTCCTTCCGCTC 60.449 63.158 0.00 0.00 0.00 5.03
961 1126 3.851051 CTGAGGCTTCAGTCCTTCC 57.149 57.895 17.29 0.00 44.74 3.46
981 1146 0.607489 TAGTAGTAGATCGCCGGCCC 60.607 60.000 23.46 10.66 0.00 5.80
990 1155 4.726583 TGCCGTTCCTCATAGTAGTAGAT 58.273 43.478 0.00 0.00 0.00 1.98
1093 1258 4.208686 GATCTCCGCCGCGAACCT 62.209 66.667 15.93 0.00 0.00 3.50
1230 1395 4.393778 GAGACGGGGTCCTGGGGA 62.394 72.222 0.48 0.00 32.18 4.81
1241 1406 4.452733 GCGTGGGGAAGGAGACGG 62.453 72.222 0.00 0.00 32.45 4.79
1569 1734 2.308690 GGTGTATCCTAGAAGAGCCGT 58.691 52.381 0.00 0.00 0.00 5.68
1665 1836 9.702494 CACAGCATCATCTGTCTAATCTAATAA 57.298 33.333 0.00 0.00 44.81 1.40
1666 1837 8.864087 ACACAGCATCATCTGTCTAATCTAATA 58.136 33.333 0.00 0.00 44.81 0.98
1687 1858 0.870393 ACAATCGCTCTTGCACACAG 59.130 50.000 0.00 0.00 39.64 3.66
1688 1859 1.798223 GTACAATCGCTCTTGCACACA 59.202 47.619 0.00 0.00 39.64 3.72
1689 1860 1.128692 GGTACAATCGCTCTTGCACAC 59.871 52.381 0.00 0.00 39.64 3.82
1690 1861 1.270571 TGGTACAATCGCTCTTGCACA 60.271 47.619 0.00 0.00 34.78 4.57
1691 1862 1.128692 GTGGTACAATCGCTCTTGCAC 59.871 52.381 0.00 0.00 44.16 4.57
1692 1863 1.438651 GTGGTACAATCGCTCTTGCA 58.561 50.000 0.00 0.00 44.16 4.08
1693 1864 0.727398 GGTGGTACAATCGCTCTTGC 59.273 55.000 0.00 0.00 44.16 4.01
1694 1865 1.732259 GTGGTGGTACAATCGCTCTTG 59.268 52.381 0.00 0.00 44.16 3.02
1699 1872 0.321298 AGTGGTGGTGGTACAATCGC 60.321 55.000 0.00 0.00 44.16 4.58
1753 1929 0.726827 GCGCAAATCTCCGTCAATCA 59.273 50.000 0.30 0.00 0.00 2.57
1754 1930 0.028110 GGCGCAAATCTCCGTCAATC 59.972 55.000 10.83 0.00 0.00 2.67
1755 1931 1.376609 GGGCGCAAATCTCCGTCAAT 61.377 55.000 10.83 0.00 0.00 2.57
1757 1933 2.435938 GGGCGCAAATCTCCGTCA 60.436 61.111 10.83 0.00 0.00 4.35
1758 1934 1.582610 TTTGGGCGCAAATCTCCGTC 61.583 55.000 23.49 0.00 0.00 4.79
1759 1935 0.965363 ATTTGGGCGCAAATCTCCGT 60.965 50.000 29.90 12.91 29.61 4.69
1760 1936 0.173255 AATTTGGGCGCAAATCTCCG 59.827 50.000 33.62 0.00 34.06 4.63
1761 1937 2.385013 AAATTTGGGCGCAAATCTCC 57.615 45.000 33.62 0.00 34.06 3.71
1762 1938 2.159667 GCAAAATTTGGGCGCAAATCTC 60.160 45.455 33.62 21.25 34.06 2.75
1763 1939 1.805943 GCAAAATTTGGGCGCAAATCT 59.194 42.857 33.62 22.72 34.06 2.40
1764 1940 1.463858 CGCAAAATTTGGGCGCAAATC 60.464 47.619 33.62 22.70 44.49 2.17
1765 1941 0.516439 CGCAAAATTTGGGCGCAAAT 59.484 45.000 29.90 29.90 44.49 2.32
1766 1942 1.937391 CGCAAAATTTGGGCGCAAA 59.063 47.368 28.27 28.27 44.49 3.68
1767 1943 3.635204 CGCAAAATTTGGGCGCAA 58.365 50.000 20.05 12.81 44.49 4.85
1858 2042 0.520404 AGTTGCTGCAAATGCTCTCG 59.480 50.000 17.80 0.00 42.66 4.04
1881 2065 3.603965 ACCCCACCACTAAACAATTCA 57.396 42.857 0.00 0.00 0.00 2.57
1888 2072 3.139397 ACATCTCAAACCCCACCACTAAA 59.861 43.478 0.00 0.00 0.00 1.85
1889 2073 2.714250 ACATCTCAAACCCCACCACTAA 59.286 45.455 0.00 0.00 0.00 2.24
1909 2132 4.886579 AGCAAAGGAAACATGAATGGAAC 58.113 39.130 0.00 0.00 0.00 3.62
1910 2133 4.021192 GGAGCAAAGGAAACATGAATGGAA 60.021 41.667 0.00 0.00 0.00 3.53
1912 2135 3.368739 GGGAGCAAAGGAAACATGAATGG 60.369 47.826 0.00 0.00 0.00 3.16
1968 2217 7.992608 ACAGAAGAAACCCTTGCAAATAAAATT 59.007 29.630 0.00 0.00 34.68 1.82
1969 2218 7.508687 ACAGAAGAAACCCTTGCAAATAAAAT 58.491 30.769 0.00 0.00 34.68 1.82
1970 2219 6.883744 ACAGAAGAAACCCTTGCAAATAAAA 58.116 32.000 0.00 0.00 34.68 1.52
1971 2220 6.478512 ACAGAAGAAACCCTTGCAAATAAA 57.521 33.333 0.00 0.00 34.68 1.40
1972 2221 7.775053 ATACAGAAGAAACCCTTGCAAATAA 57.225 32.000 0.00 0.00 34.68 1.40
1973 2222 7.450014 TGAATACAGAAGAAACCCTTGCAAATA 59.550 33.333 0.00 0.00 34.68 1.40
1974 2223 6.267471 TGAATACAGAAGAAACCCTTGCAAAT 59.733 34.615 0.00 0.00 34.68 2.32
1981 2230 5.770162 CCAGTTTGAATACAGAAGAAACCCT 59.230 40.000 0.00 0.00 0.00 4.34
2025 2277 0.179056 ACCGTAGCAGTGCAGTGTTT 60.179 50.000 22.22 13.48 0.00 2.83
2096 2351 0.306533 CGAACCACAAACCCAGAACG 59.693 55.000 0.00 0.00 0.00 3.95
2111 2366 4.151689 TCGAACTCATCAAAATCCACGAAC 59.848 41.667 0.00 0.00 0.00 3.95
2115 2370 4.731773 GCCATCGAACTCATCAAAATCCAC 60.732 45.833 0.00 0.00 0.00 4.02
2117 2372 3.546815 CGCCATCGAACTCATCAAAATCC 60.547 47.826 0.00 0.00 38.10 3.01
2126 2381 1.006825 CGAACACGCCATCGAACTCA 61.007 55.000 0.00 0.00 41.43 3.41
2145 2400 1.967319 ATCACCCACATGTTATCCGC 58.033 50.000 0.00 0.00 0.00 5.54
2146 2401 6.639563 TGATATATCACCCACATGTTATCCG 58.360 40.000 11.49 0.00 0.00 4.18
2147 2402 6.540189 GCTGATATATCACCCACATGTTATCC 59.460 42.308 11.49 0.00 32.50 2.59
2148 2403 6.256539 CGCTGATATATCACCCACATGTTATC 59.743 42.308 11.49 0.00 32.50 1.75
2149 2404 6.108687 CGCTGATATATCACCCACATGTTAT 58.891 40.000 11.49 0.00 32.50 1.89
2160 2415 4.088638 CGCAGTACAACGCTGATATATCAC 59.911 45.833 11.49 8.00 36.12 3.06
2164 2419 3.703286 ACGCAGTACAACGCTGATATA 57.297 42.857 7.38 0.00 41.94 0.86
2211 2467 9.031360 CAGAGAAGCCATCAATGAATAAAAATG 57.969 33.333 0.00 0.00 0.00 2.32
2212 2468 8.202137 CCAGAGAAGCCATCAATGAATAAAAAT 58.798 33.333 0.00 0.00 0.00 1.82
2222 2478 3.087031 CACAACCAGAGAAGCCATCAAT 58.913 45.455 0.00 0.00 0.00 2.57
2229 2485 2.328099 CCGGCACAACCAGAGAAGC 61.328 63.158 0.00 0.00 39.03 3.86
2230 2486 0.671781 CTCCGGCACAACCAGAGAAG 60.672 60.000 0.00 0.00 44.75 2.85
2231 2487 1.371183 CTCCGGCACAACCAGAGAA 59.629 57.895 0.00 0.00 44.75 2.87
2232 2488 1.407656 AACTCCGGCACAACCAGAGA 61.408 55.000 0.00 0.00 44.75 3.10
2241 2497 0.034337 TTGTCACCTAACTCCGGCAC 59.966 55.000 0.00 0.00 0.00 5.01
2254 2510 2.791004 GCTTGTCAGCAACATTTGTCAC 59.209 45.455 0.00 0.00 46.49 3.67
2267 2523 6.309712 TGAAGAATCTTTTGAGCTTGTCAG 57.690 37.500 0.00 0.00 36.21 3.51
2387 2653 7.763071 GGTGATATACGTGTCCTTTTATATCCC 59.237 40.741 0.00 1.23 34.81 3.85
2388 2654 8.308931 TGGTGATATACGTGTCCTTTTATATCC 58.691 37.037 0.00 0.00 34.81 2.59
2398 2664 8.333186 GTTCTTTTTATGGTGATATACGTGTCC 58.667 37.037 0.00 0.00 0.00 4.02
2408 2674 9.216117 GTGTAGTAGTGTTCTTTTTATGGTGAT 57.784 33.333 0.00 0.00 0.00 3.06
2409 2675 8.426489 AGTGTAGTAGTGTTCTTTTTATGGTGA 58.574 33.333 0.00 0.00 0.00 4.02
2410 2676 8.495949 CAGTGTAGTAGTGTTCTTTTTATGGTG 58.504 37.037 0.00 0.00 0.00 4.17
2411 2677 7.172703 GCAGTGTAGTAGTGTTCTTTTTATGGT 59.827 37.037 0.00 0.00 32.06 3.55
2412 2678 7.387948 AGCAGTGTAGTAGTGTTCTTTTTATGG 59.612 37.037 0.00 0.00 32.06 2.74
2413 2679 8.311650 AGCAGTGTAGTAGTGTTCTTTTTATG 57.688 34.615 0.00 0.00 32.06 1.90
2414 2680 9.420551 GTAGCAGTGTAGTAGTGTTCTTTTTAT 57.579 33.333 0.00 0.00 32.06 1.40
2415 2681 8.415553 TGTAGCAGTGTAGTAGTGTTCTTTTTA 58.584 33.333 0.00 0.00 32.06 1.52
2416 2682 7.270047 TGTAGCAGTGTAGTAGTGTTCTTTTT 58.730 34.615 0.00 0.00 32.06 1.94
2421 2687 5.048921 TGACTGTAGCAGTGTAGTAGTGTTC 60.049 44.000 6.50 0.00 45.44 3.18
2432 2698 3.188667 TCTCGTTACTGACTGTAGCAGTG 59.811 47.826 6.50 0.00 45.44 3.66
2438 2704 8.743085 AGGTATTTATCTCGTTACTGACTGTA 57.257 34.615 0.00 0.00 0.00 2.74
2439 2705 7.642082 AGGTATTTATCTCGTTACTGACTGT 57.358 36.000 0.00 0.00 0.00 3.55
2442 2708 9.408069 CCAATAGGTATTTATCTCGTTACTGAC 57.592 37.037 0.00 0.00 0.00 3.51
2443 2709 8.086522 GCCAATAGGTATTTATCTCGTTACTGA 58.913 37.037 0.00 0.00 37.19 3.41
2444 2710 7.331193 GGCCAATAGGTATTTATCTCGTTACTG 59.669 40.741 0.00 0.00 37.19 2.74
2445 2711 7.384477 GGCCAATAGGTATTTATCTCGTTACT 58.616 38.462 0.00 0.00 37.19 2.24
2446 2712 6.592994 GGGCCAATAGGTATTTATCTCGTTAC 59.407 42.308 4.39 0.00 37.19 2.50
2447 2713 6.270463 TGGGCCAATAGGTATTTATCTCGTTA 59.730 38.462 2.13 0.00 37.19 3.18
2448 2714 5.072600 TGGGCCAATAGGTATTTATCTCGTT 59.927 40.000 2.13 0.00 37.19 3.85
2449 2715 4.595781 TGGGCCAATAGGTATTTATCTCGT 59.404 41.667 2.13 0.00 37.19 4.18
2450 2716 4.935808 GTGGGCCAATAGGTATTTATCTCG 59.064 45.833 8.40 0.00 37.19 4.04
2451 2717 5.222048 TGGTGGGCCAATAGGTATTTATCTC 60.222 44.000 8.40 0.00 42.83 2.75
2452 2718 4.667858 TGGTGGGCCAATAGGTATTTATCT 59.332 41.667 8.40 0.00 42.83 1.98
2453 2719 4.993028 TGGTGGGCCAATAGGTATTTATC 58.007 43.478 8.40 0.00 42.83 1.75
2503 2769 4.724279 AGTAATGTGGTTTGGAGGAAGT 57.276 40.909 0.00 0.00 0.00 3.01
2506 2772 6.012858 AGTGATAAGTAATGTGGTTTGGAGGA 60.013 38.462 0.00 0.00 0.00 3.71
2510 2776 7.630242 ATCAGTGATAAGTAATGTGGTTTGG 57.370 36.000 3.05 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.