Multiple sequence alignment - TraesCS3D01G268700

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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 TraesCS3D01G268700 chr3D 100.000 3422 0 0 1 3422 373330637 373327216 0.000000e+00 6320
1 TraesCS3D01G268700 chr3D 79.432 739 125 16 52 772 424894806 424895535 6.590000e-137 497
2 TraesCS3D01G268700 chr3B 89.835 1938 149 30 1 1906 487051211 487049290 0.000000e+00 2444
3 TraesCS3D01G268700 chr3B 93.106 1378 69 14 2057 3422 487049193 487047830 0.000000e+00 1995
4 TraesCS3D01G268700 chr3B 77.645 586 116 10 230 808 183789433 183790010 3.270000e-90 342
5 TraesCS3D01G268700 chr3A 92.743 1378 73 13 2053 3422 494729143 494727785 0.000000e+00 1965
6 TraesCS3D01G268700 chr3A 89.383 1281 96 22 651 1905 494730544 494729278 0.000000e+00 1576
7 TraesCS3D01G268700 chr6B 81.860 656 95 18 52 692 575324457 575325103 6.500000e-147 531
8 TraesCS3D01G268700 chr6B 78.116 658 127 13 39 689 480688539 480689186 5.320000e-108 401
9 TraesCS3D01G268700 chr6B 82.803 157 25 2 1908 2064 69443524 69443678 4.600000e-29 139
10 TraesCS3D01G268700 chr5A 80.199 702 110 16 43 726 353155745 353156435 1.830000e-137 499
11 TraesCS3D01G268700 chr5A 89.172 157 15 2 1907 2063 86662172 86662018 9.690000e-46 195
12 TraesCS3D01G268700 chr5A 83.333 156 24 2 1907 2062 366635481 366635328 3.560000e-30 143
13 TraesCS3D01G268700 chr2D 78.805 703 125 16 52 741 644901973 644902664 5.210000e-123 451
14 TraesCS3D01G268700 chr6D 79.353 649 121 9 47 689 340201856 340201215 8.710000e-121 444
15 TraesCS3D01G268700 chr6D 80.000 610 97 19 39 633 385225408 385226007 8.780000e-116 427
16 TraesCS3D01G268700 chr2B 77.304 727 137 18 58 770 790640557 790639845 1.480000e-108 403
17 TraesCS3D01G268700 chr7D 86.452 155 18 3 1908 2062 404056814 404056965 2.110000e-37 167
18 TraesCS3D01G268700 chr7D 83.439 157 20 6 1904 2059 10723451 10723602 1.280000e-29 141
19 TraesCS3D01G268700 chr4D 84.076 157 23 2 1908 2064 108627597 108627751 2.130000e-32 150
20 TraesCS3D01G268700 chr4D 82.803 157 25 2 1908 2064 280180797 280180643 4.600000e-29 139
21 TraesCS3D01G268700 chr7A 83.333 162 23 4 1903 2062 609383405 609383564 2.750000e-31 147
22 TraesCS3D01G268700 chr1A 82.927 164 23 5 1902 2062 298614240 298614401 3.560000e-30 143


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 TraesCS3D01G268700 chr3D 373327216 373330637 3421 True 6320.0 6320 100.0000 1 3422 1 chr3D.!!$R1 3421
1 TraesCS3D01G268700 chr3D 424894806 424895535 729 False 497.0 497 79.4320 52 772 1 chr3D.!!$F1 720
2 TraesCS3D01G268700 chr3B 487047830 487051211 3381 True 2219.5 2444 91.4705 1 3422 2 chr3B.!!$R1 3421
3 TraesCS3D01G268700 chr3B 183789433 183790010 577 False 342.0 342 77.6450 230 808 1 chr3B.!!$F1 578
4 TraesCS3D01G268700 chr3A 494727785 494730544 2759 True 1770.5 1965 91.0630 651 3422 2 chr3A.!!$R1 2771
5 TraesCS3D01G268700 chr6B 575324457 575325103 646 False 531.0 531 81.8600 52 692 1 chr6B.!!$F3 640
6 TraesCS3D01G268700 chr6B 480688539 480689186 647 False 401.0 401 78.1160 39 689 1 chr6B.!!$F2 650
7 TraesCS3D01G268700 chr5A 353155745 353156435 690 False 499.0 499 80.1990 43 726 1 chr5A.!!$F1 683
8 TraesCS3D01G268700 chr2D 644901973 644902664 691 False 451.0 451 78.8050 52 741 1 chr2D.!!$F1 689
9 TraesCS3D01G268700 chr6D 340201215 340201856 641 True 444.0 444 79.3530 47 689 1 chr6D.!!$R1 642
10 TraesCS3D01G268700 chr6D 385225408 385226007 599 False 427.0 427 80.0000 39 633 1 chr6D.!!$F1 594
11 TraesCS3D01G268700 chr2B 790639845 790640557 712 True 403.0 403 77.3040 58 770 1 chr2B.!!$R1 712

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
318 333 0.394565 CAATGGGACCCCGAGATCTC 59.605 60.0 13.05 13.05 39.42 2.75 F
881 920 0.446222 GCAAAGCAGGCGTAAATCGA 59.554 50.0 0.00 0.00 42.86 3.59 F
1558 1627 0.709992 TGAATTTTGAGGGGAGGGGG 59.290 55.0 0.00 0.00 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1608 0.709992 CCCCCTCCCCTCAAAATTCA 59.290 55.000 0.0 0.0 0.00 2.57 R
2413 2513 0.178873 TCCCCCAGAAACTAGGCAGT 60.179 55.000 0.0 0.0 36.19 4.40 R
2972 3077 1.273324 ACAGAGGAGGGTCAAGGTAGG 60.273 57.143 0.0 0.0 0.00 3.18 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
46 47 1.173043 CTTTGGATTTGGCAGCGGTA 58.827 50.000 0.00 0.00 0.00 4.02
54 56 0.463654 TTGGCAGCGGTATCCATGTC 60.464 55.000 8.35 0.00 0.00 3.06
98 104 4.161102 AGCTCCTCCTTACAACTACACTT 58.839 43.478 0.00 0.00 0.00 3.16
134 141 6.611236 TCATTAGAACATGGACCACTATCTGA 59.389 38.462 12.70 6.97 0.00 3.27
144 151 5.305386 TGGACCACTATCTGATTGATGGTAG 59.695 44.000 18.27 3.98 43.63 3.18
180 187 4.748892 ACTACATTCGTCAAGACCATCTG 58.251 43.478 0.00 0.00 0.00 2.90
185 192 1.546029 TCGTCAAGACCATCTGTGAGG 59.454 52.381 0.00 0.00 0.00 3.86
227 241 6.655425 AGCTCACTTTAACCAAAGATAAGGAC 59.345 38.462 4.23 0.00 43.32 3.85
254 268 3.463048 AGGATGTGGAGAAGGCATTTT 57.537 42.857 0.00 0.00 0.00 1.82
262 276 2.560105 GGAGAAGGCATTTTGAGTGCTT 59.440 45.455 0.00 0.00 42.16 3.91
268 282 2.991190 GGCATTTTGAGTGCTTCATGTG 59.009 45.455 0.00 0.00 42.16 3.21
310 325 1.474330 CTGCTAAACAATGGGACCCC 58.526 55.000 8.45 2.69 0.00 4.95
318 333 0.394565 CAATGGGACCCCGAGATCTC 59.605 60.000 13.05 13.05 39.42 2.75
342 361 6.382282 TCAGGGGAGATGATGACATATATGAC 59.618 42.308 19.63 13.55 36.82 3.06
401 420 3.078837 GTTGCCCGAGGTCTGAAATTTA 58.921 45.455 0.00 0.00 0.00 1.40
436 455 5.370584 TGATCCTATCCAACTTCCACATCAT 59.629 40.000 0.00 0.00 0.00 2.45
479 498 6.592798 AGTTTGTTCAAATGCATCAACAAG 57.407 33.333 21.44 3.74 39.31 3.16
511 530 4.083855 CGAGCAACTTATGAGCAGTTCAAA 60.084 41.667 0.00 0.00 39.77 2.69
515 534 6.039717 AGCAACTTATGAGCAGTTCAAAGAAA 59.960 34.615 12.72 0.00 39.77 2.52
516 535 6.865205 GCAACTTATGAGCAGTTCAAAGAAAT 59.135 34.615 12.72 0.00 39.77 2.17
755 786 4.128580 TGGATGACCAGCTTCCGA 57.871 55.556 0.00 0.00 42.32 4.55
779 811 2.048503 GTCCGTGAACCCAGTCCG 60.049 66.667 0.00 0.00 0.00 4.79
809 841 2.203470 TAATGTCCGTTTTGGGGGTC 57.797 50.000 0.00 0.00 38.76 4.46
815 847 2.908428 GTTTTGGGGGTCGGCGTT 60.908 61.111 6.85 0.00 0.00 4.84
817 849 1.302671 TTTTGGGGGTCGGCGTTAG 60.303 57.895 6.85 0.00 0.00 2.34
844 876 6.436843 CACCCTTGTGGAAGACATTATAAC 57.563 41.667 0.00 0.00 38.90 1.89
845 877 6.180472 CACCCTTGTGGAAGACATTATAACT 58.820 40.000 0.00 0.00 38.90 2.24
868 907 0.796927 GTCCCGTCTTAGTGCAAAGC 59.203 55.000 0.00 0.00 0.00 3.51
881 920 0.446222 GCAAAGCAGGCGTAAATCGA 59.554 50.000 0.00 0.00 42.86 3.59
963 1004 3.138625 CACTGACACAGGACGGGT 58.861 61.111 0.00 0.00 35.51 5.28
969 1010 2.377628 GACACAGGACGGGTCTGCAA 62.378 60.000 0.00 0.00 35.78 4.08
1176 1217 0.815734 CCTTCTCCCGCTCGAGTTTA 59.184 55.000 15.13 0.00 0.00 2.01
1221 1263 1.734465 CAGTGACCGAGAATGCTTTCC 59.266 52.381 8.62 0.72 31.84 3.13
1287 1329 4.586235 GGGCTGCAGGTGGTGTGT 62.586 66.667 17.12 0.00 0.00 3.72
1426 1470 7.885399 GGATGAAGAAGGTATACAATGCCTAAT 59.115 37.037 5.01 0.00 45.18 1.73
1451 1495 1.531423 GCGTATCCCTCTATCCGTCA 58.469 55.000 0.00 0.00 0.00 4.35
1452 1496 1.884579 GCGTATCCCTCTATCCGTCAA 59.115 52.381 0.00 0.00 0.00 3.18
1453 1497 2.095161 GCGTATCCCTCTATCCGTCAAG 60.095 54.545 0.00 0.00 0.00 3.02
1454 1498 3.147629 CGTATCCCTCTATCCGTCAAGT 58.852 50.000 0.00 0.00 0.00 3.16
1455 1499 3.568853 CGTATCCCTCTATCCGTCAAGTT 59.431 47.826 0.00 0.00 0.00 2.66
1456 1500 4.037684 CGTATCCCTCTATCCGTCAAGTTT 59.962 45.833 0.00 0.00 0.00 2.66
1458 1502 2.093658 TCCCTCTATCCGTCAAGTTTGC 60.094 50.000 0.00 0.00 0.00 3.68
1459 1503 2.280628 CCTCTATCCGTCAAGTTTGCC 58.719 52.381 0.00 0.00 0.00 4.52
1539 1608 2.026356 TGCTGTAATGCTGTGTATGGGT 60.026 45.455 0.00 0.00 0.00 4.51
1552 1621 3.447229 GTGTATGGGTGAATTTTGAGGGG 59.553 47.826 0.00 0.00 0.00 4.79
1553 1622 3.335183 TGTATGGGTGAATTTTGAGGGGA 59.665 43.478 0.00 0.00 0.00 4.81
1558 1627 0.709992 TGAATTTTGAGGGGAGGGGG 59.290 55.000 0.00 0.00 0.00 5.40
1644 1713 7.595819 TTCTCCACTTGAAATACATTTTGGT 57.404 32.000 4.04 0.00 0.00 3.67
1700 1769 7.619965 TGTCAGTGTAGATGGATTTGATGTAA 58.380 34.615 0.00 0.00 0.00 2.41
1803 1872 1.626686 TGCCCACAAAACATCCGAAT 58.373 45.000 0.00 0.00 0.00 3.34
1813 1882 4.310022 AAACATCCGAATAAGGGGACAA 57.690 40.909 0.00 0.00 34.58 3.18
1846 1915 3.319689 CCACCAAATTTAGTTTCCGTGGT 59.680 43.478 7.42 0.00 39.86 4.16
1872 1941 9.817809 TGTACTTCATCTGAATAATAGGTGTTC 57.182 33.333 0.00 0.00 33.01 3.18
1878 1947 7.981789 TCATCTGAATAATAGGTGTTCTGTGTC 59.018 37.037 0.00 0.00 0.00 3.67
1883 1952 8.946085 TGAATAATAGGTGTTCTGTGTCATTTC 58.054 33.333 0.00 0.00 0.00 2.17
1892 1961 7.041098 GGTGTTCTGTGTCATTTCAGTAAATCT 60.041 37.037 0.00 0.00 32.87 2.40
1897 1966 9.166173 TCTGTGTCATTTCAGTAAATCTAATGG 57.834 33.333 0.00 0.00 32.87 3.16
1901 1970 8.407832 TGTCATTTCAGTAAATCTAATGGCATG 58.592 33.333 0.00 0.00 34.09 4.06
1915 1984 7.224297 TCTAATGGCATGTAAAATACTCCCTC 58.776 38.462 0.00 0.00 0.00 4.30
1916 1985 4.164843 TGGCATGTAAAATACTCCCTCC 57.835 45.455 0.00 0.00 0.00 4.30
1917 1986 3.139077 GGCATGTAAAATACTCCCTCCG 58.861 50.000 0.00 0.00 0.00 4.63
1920 1989 4.638865 GCATGTAAAATACTCCCTCCGTTT 59.361 41.667 0.00 0.00 0.00 3.60
1921 1990 5.124936 GCATGTAAAATACTCCCTCCGTTTT 59.875 40.000 0.00 0.00 0.00 2.43
1923 1992 6.806388 TGTAAAATACTCCCTCCGTTTTTC 57.194 37.500 0.00 0.00 0.00 2.29
1924 1993 6.536447 TGTAAAATACTCCCTCCGTTTTTCT 58.464 36.000 0.00 0.00 0.00 2.52
1926 1995 8.323567 TGTAAAATACTCCCTCCGTTTTTCTAT 58.676 33.333 0.00 0.00 0.00 1.98
1927 1996 9.170734 GTAAAATACTCCCTCCGTTTTTCTATT 57.829 33.333 0.00 0.00 0.00 1.73
1934 2003 8.935741 ACTCCCTCCGTTTTTCTATTATAAGAT 58.064 33.333 0.00 0.00 0.00 2.40
1936 2005 8.711170 TCCCTCCGTTTTTCTATTATAAGATGT 58.289 33.333 0.00 0.00 0.00 3.06
1937 2006 9.338622 CCCTCCGTTTTTCTATTATAAGATGTT 57.661 33.333 0.00 0.00 0.00 2.71
1955 2024 8.438676 AAGATGTTTTGGATATTTCCGTAGAG 57.561 34.615 0.00 0.00 45.89 2.43
1956 2025 7.792032 AGATGTTTTGGATATTTCCGTAGAGA 58.208 34.615 0.00 0.00 45.89 3.10
1957 2026 7.711339 AGATGTTTTGGATATTTCCGTAGAGAC 59.289 37.037 0.00 0.00 45.89 3.36
1958 2027 6.942976 TGTTTTGGATATTTCCGTAGAGACT 58.057 36.000 0.00 0.00 45.89 3.24
1959 2028 8.070034 TGTTTTGGATATTTCCGTAGAGACTA 57.930 34.615 0.00 0.00 45.89 2.59
1960 2029 7.977853 TGTTTTGGATATTTCCGTAGAGACTAC 59.022 37.037 0.00 0.00 45.89 2.73
1961 2030 7.649533 TTTGGATATTTCCGTAGAGACTACA 57.350 36.000 9.14 0.00 45.89 2.74
1962 2031 7.834881 TTGGATATTTCCGTAGAGACTACAT 57.165 36.000 9.14 0.00 45.89 2.29
1963 2032 8.929260 TTGGATATTTCCGTAGAGACTACATA 57.071 34.615 9.14 1.18 45.89 2.29
1964 2033 8.332996 TGGATATTTCCGTAGAGACTACATAC 57.667 38.462 9.14 0.00 45.89 2.39
1965 2034 7.940688 TGGATATTTCCGTAGAGACTACATACA 59.059 37.037 9.14 0.00 45.89 2.29
1966 2035 8.452534 GGATATTTCCGTAGAGACTACATACAG 58.547 40.741 9.14 0.00 30.72 2.74
1967 2036 9.217278 GATATTTCCGTAGAGACTACATACAGA 57.783 37.037 9.14 0.00 0.00 3.41
1968 2037 6.674694 TTTCCGTAGAGACTACATACAGAC 57.325 41.667 9.14 0.00 0.00 3.51
1969 2038 4.701765 TCCGTAGAGACTACATACAGACC 58.298 47.826 9.14 0.00 0.00 3.85
1970 2039 4.162888 TCCGTAGAGACTACATACAGACCA 59.837 45.833 9.14 0.00 0.00 4.02
1971 2040 4.880120 CCGTAGAGACTACATACAGACCAA 59.120 45.833 9.14 0.00 0.00 3.67
1972 2041 5.356190 CCGTAGAGACTACATACAGACCAAA 59.644 44.000 9.14 0.00 0.00 3.28
1973 2042 6.127814 CCGTAGAGACTACATACAGACCAAAA 60.128 42.308 9.14 0.00 0.00 2.44
1974 2043 7.416438 CCGTAGAGACTACATACAGACCAAAAT 60.416 40.741 9.14 0.00 0.00 1.82
1975 2044 7.432545 CGTAGAGACTACATACAGACCAAAATG 59.567 40.741 9.14 0.00 0.00 2.32
1976 2045 7.482169 AGAGACTACATACAGACCAAAATGA 57.518 36.000 0.00 0.00 0.00 2.57
1977 2046 7.551585 AGAGACTACATACAGACCAAAATGAG 58.448 38.462 0.00 0.00 0.00 2.90
1978 2047 7.179338 AGAGACTACATACAGACCAAAATGAGT 59.821 37.037 0.00 0.00 0.00 3.41
1979 2048 7.099764 AGACTACATACAGACCAAAATGAGTG 58.900 38.462 0.00 0.00 0.00 3.51
1980 2049 7.004555 ACTACATACAGACCAAAATGAGTGA 57.995 36.000 0.00 0.00 0.00 3.41
1981 2050 7.450074 ACTACATACAGACCAAAATGAGTGAA 58.550 34.615 0.00 0.00 0.00 3.18
1982 2051 6.560253 ACATACAGACCAAAATGAGTGAAC 57.440 37.500 0.00 0.00 0.00 3.18
1983 2052 6.061441 ACATACAGACCAAAATGAGTGAACA 58.939 36.000 0.00 0.00 0.00 3.18
1984 2053 6.545666 ACATACAGACCAAAATGAGTGAACAA 59.454 34.615 0.00 0.00 0.00 2.83
1985 2054 5.913137 ACAGACCAAAATGAGTGAACAAA 57.087 34.783 0.00 0.00 0.00 2.83
1986 2055 5.650543 ACAGACCAAAATGAGTGAACAAAC 58.349 37.500 0.00 0.00 0.00 2.93
1987 2056 5.184864 ACAGACCAAAATGAGTGAACAAACA 59.815 36.000 0.00 0.00 0.00 2.83
1991 2060 5.167121 CCAAAATGAGTGAACAAACACACA 58.833 37.500 0.00 0.00 42.98 3.72
1992 2061 5.636965 CCAAAATGAGTGAACAAACACACAA 59.363 36.000 0.00 0.00 42.37 3.33
1997 2066 6.702972 TGAGTGAACAAACACACAAAAATG 57.297 33.333 0.00 0.00 42.45 2.32
2004 2073 5.587289 ACAAACACACAAAAATGCGTCTAT 58.413 33.333 0.00 0.00 0.00 1.98
2014 2083 8.341903 CACAAAAATGCGTCTATATACATCCAA 58.658 33.333 0.00 0.00 0.00 3.53
2019 2088 8.846943 AATGCGTCTATATACATCCAATTCAA 57.153 30.769 0.00 0.00 0.00 2.69
2020 2089 7.889589 TGCGTCTATATACATCCAATTCAAG 57.110 36.000 0.00 0.00 0.00 3.02
2021 2090 7.666623 TGCGTCTATATACATCCAATTCAAGA 58.333 34.615 0.00 0.00 0.00 3.02
2022 2091 8.147704 TGCGTCTATATACATCCAATTCAAGAA 58.852 33.333 0.00 0.00 0.00 2.52
2023 2092 8.988934 GCGTCTATATACATCCAATTCAAGAAA 58.011 33.333 0.00 0.00 0.00 2.52
2075 2173 4.725790 ACGGAGTACAAGTTATGGGTAC 57.274 45.455 0.00 0.00 41.94 3.34
2076 2174 4.088634 ACGGAGTACAAGTTATGGGTACA 58.911 43.478 0.00 0.00 41.94 2.90
2078 2176 5.107133 CGGAGTACAAGTTATGGGTACAAG 58.893 45.833 0.00 0.00 39.78 3.16
2080 2178 5.425630 GAGTACAAGTTATGGGTACAAGGG 58.574 45.833 0.00 0.00 39.78 3.95
2093 2191 1.620822 ACAAGGGTGGTTTCATCTGC 58.379 50.000 0.00 0.00 0.00 4.26
2144 2244 8.424133 AGCAATCAATACCAGAAGTTTCTTTTT 58.576 29.630 0.00 0.00 34.74 1.94
2145 2245 9.691362 GCAATCAATACCAGAAGTTTCTTTTTA 57.309 29.630 0.00 0.00 34.74 1.52
2162 2262 6.943981 TCTTTTTATACGAGATCAAATGCCG 58.056 36.000 0.00 0.00 0.00 5.69
2211 2311 3.327757 TCAGAGCCCTTGAAAAGCTTAGA 59.672 43.478 0.00 0.00 44.44 2.10
2304 2404 2.741878 CGACAAGACAGTGAAGGTTGGT 60.742 50.000 0.00 0.00 0.00 3.67
2394 2494 1.354101 TCCGTGGTTGGTATGTTCCT 58.646 50.000 0.00 0.00 0.00 3.36
2400 2500 3.380320 GTGGTTGGTATGTTCCTAATGCC 59.620 47.826 0.00 0.00 0.00 4.40
2413 2513 0.607762 TAATGCCGAACCTGCTGCAA 60.608 50.000 3.02 0.00 37.27 4.08
2436 2536 0.824759 CCTAGTTTCTGGGGGAGTCG 59.175 60.000 0.00 0.00 0.00 4.18
2441 2541 1.003233 GTTTCTGGGGGAGTCGTCATT 59.997 52.381 0.00 0.00 0.00 2.57
2444 2544 0.391661 CTGGGGGAGTCGTCATTGTG 60.392 60.000 0.00 0.00 0.00 3.33
2447 2547 1.065418 GGGGGAGTCGTCATTGTGAAT 60.065 52.381 0.00 0.00 0.00 2.57
2457 2557 2.410730 GTCATTGTGAATTTGCAGCAGC 59.589 45.455 0.00 0.00 42.57 5.25
2463 2563 2.477754 GTGAATTTGCAGCAGCTTTTCC 59.522 45.455 1.76 0.00 42.74 3.13
2509 2609 5.877564 TGGACAGCATATGTTATTGAACGAA 59.122 36.000 4.29 0.00 44.17 3.85
2557 2657 1.202770 GGCAAGTGTTCTGGTACTGGT 60.203 52.381 0.00 0.00 0.00 4.00
2575 2675 4.755123 ACTGGTTACTGTGTTTATGTGCTC 59.245 41.667 0.00 0.00 0.00 4.26
2581 2681 3.618594 ACTGTGTTTATGTGCTCGCTATG 59.381 43.478 0.00 0.00 0.00 2.23
2582 2682 2.351418 TGTGTTTATGTGCTCGCTATGC 59.649 45.455 0.00 0.00 0.00 3.14
2583 2683 2.351418 GTGTTTATGTGCTCGCTATGCA 59.649 45.455 0.00 0.00 38.19 3.96
2584 2684 2.609002 TGTTTATGTGCTCGCTATGCAG 59.391 45.455 0.00 0.00 41.41 4.41
2585 2685 2.602257 TTATGTGCTCGCTATGCAGT 57.398 45.000 0.00 0.00 41.41 4.40
2586 2686 3.726291 TTATGTGCTCGCTATGCAGTA 57.274 42.857 0.00 0.00 41.41 2.74
2587 2687 2.145958 ATGTGCTCGCTATGCAGTAG 57.854 50.000 0.00 0.00 41.41 2.57
2588 2688 1.102978 TGTGCTCGCTATGCAGTAGA 58.897 50.000 0.00 0.00 41.41 2.59
2589 2689 1.476488 TGTGCTCGCTATGCAGTAGAA 59.524 47.619 0.00 0.00 41.41 2.10
2596 2696 2.033927 CGCTATGCAGTAGAAGCTCTGA 59.966 50.000 4.41 0.00 34.02 3.27
2597 2697 3.489908 CGCTATGCAGTAGAAGCTCTGAA 60.490 47.826 4.41 0.00 34.02 3.02
2601 2701 4.071961 TGCAGTAGAAGCTCTGAAACAA 57.928 40.909 4.41 0.00 34.02 2.83
2602 2702 4.645535 TGCAGTAGAAGCTCTGAAACAAT 58.354 39.130 4.41 0.00 34.02 2.71
2655 2755 8.026607 CCTCTGTTGTAAAACTTCAAACTGAAA 58.973 33.333 0.00 0.00 35.73 2.69
2689 2789 7.301868 TGTATGGTGTATGCAGATATCTTCA 57.698 36.000 7.54 7.54 0.00 3.02
2737 2837 4.810191 TGCTTTCTCTCCTTACCTTCTC 57.190 45.455 0.00 0.00 0.00 2.87
2768 2868 5.995897 TGAAATGGATATGCATCTCTCACAG 59.004 40.000 10.42 0.00 0.00 3.66
2787 2887 5.880332 TCACAGCTGTTTTCTTTTGTACTCT 59.120 36.000 18.94 0.00 0.00 3.24
2833 2938 8.214364 GGAAAAGACATATAATCCTTCCTGAGT 58.786 37.037 9.50 0.00 30.80 3.41
2946 3051 6.213600 ACAGATATGACCCTAGTGAACTTGTT 59.786 38.462 0.00 0.00 0.00 2.83
3061 3166 3.673543 TGGTTCTGTAAAACCCACCTT 57.326 42.857 3.51 0.00 46.81 3.50
3062 3167 3.983821 TGGTTCTGTAAAACCCACCTTT 58.016 40.909 3.51 0.00 46.81 3.11
3094 3199 5.088680 TGTAACCGTACCCCTATCTTTTG 57.911 43.478 0.00 0.00 0.00 2.44
3165 3270 3.069016 TGACGTTTCTCTTAACTGGAGCA 59.931 43.478 0.00 0.00 0.00 4.26
3192 3297 6.369065 CCTGAGACTGGTTCAATACTGTTTAC 59.631 42.308 0.00 0.00 0.00 2.01
3198 3304 8.611654 ACTGGTTCAATACTGTTTACGTAATT 57.388 30.769 9.18 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.748493 GATACCGCTGCCAAATCCAAA 59.252 47.619 0.00 0.00 0.00 3.28
29 30 1.388547 GATACCGCTGCCAAATCCAA 58.611 50.000 0.00 0.00 0.00 3.53
46 47 3.110705 AGTCAACCTAGCAGACATGGAT 58.889 45.455 0.00 0.00 34.80 3.41
54 56 4.537135 TGTCCTTTAGTCAACCTAGCAG 57.463 45.455 0.00 0.00 0.00 4.24
87 93 5.299028 TGATGCACATTGAAAGTGTAGTTGT 59.701 36.000 2.38 0.00 39.17 3.32
98 104 6.377712 TCCATGTTCTAATGATGCACATTGAA 59.622 34.615 18.73 16.45 46.93 2.69
134 141 6.506661 TCCATAGAGGATAGCTACCATCAAT 58.493 40.000 1.97 0.00 43.07 2.57
227 241 3.432890 GCCTTCTCCACATCCTTTCTAGG 60.433 52.174 0.00 0.00 43.46 3.02
254 268 3.734597 GCAAAACACACATGAAGCACTCA 60.735 43.478 0.00 0.00 38.81 3.41
262 276 3.865011 ACAACTGCAAAACACACATGA 57.135 38.095 0.00 0.00 0.00 3.07
268 282 3.551485 GTCCATGAACAACTGCAAAACAC 59.449 43.478 0.00 0.00 0.00 3.32
318 333 6.407865 GGTCATATATGTCATCATCTCCCCTG 60.408 46.154 12.42 0.00 35.70 4.45
386 405 6.403636 CCCATGTTCTTAAATTTCAGACCTCG 60.404 42.308 1.48 0.00 0.00 4.63
401 420 4.047166 TGGATAGGATCACCCATGTTCTT 58.953 43.478 0.00 0.00 37.41 2.52
479 498 1.355971 TAAGTTGCTCGATGCCGAAC 58.644 50.000 4.73 4.04 45.04 3.95
511 530 9.962783 GCTTATAGATGCTCAATCAAAATTTCT 57.037 29.630 0.00 0.00 37.81 2.52
515 534 6.488006 ACCGCTTATAGATGCTCAATCAAAAT 59.512 34.615 0.00 0.00 37.81 1.82
516 535 5.822519 ACCGCTTATAGATGCTCAATCAAAA 59.177 36.000 0.00 0.00 37.81 2.44
624 645 8.731605 TCAAATGCGACAGTGGTTATAATTTAA 58.268 29.630 0.00 0.00 0.00 1.52
625 646 8.270080 TCAAATGCGACAGTGGTTATAATTTA 57.730 30.769 0.00 0.00 0.00 1.40
626 647 7.151999 TCAAATGCGACAGTGGTTATAATTT 57.848 32.000 0.00 0.00 0.00 1.82
771 802 2.762535 ATATTTATCCGCGGACTGGG 57.237 50.000 33.75 0.00 0.00 4.45
813 845 3.323979 TCTTCCACAAGGGTGTCTCTAAC 59.676 47.826 0.00 0.00 43.71 2.34
815 847 2.897969 GTCTTCCACAAGGGTGTCTCTA 59.102 50.000 0.00 0.00 43.71 2.43
817 849 1.416401 TGTCTTCCACAAGGGTGTCTC 59.584 52.381 0.00 0.00 43.71 3.36
842 874 3.322828 TGCACTAAGACGGGACTAAAGTT 59.677 43.478 0.00 0.00 0.00 2.66
844 876 3.587797 TGCACTAAGACGGGACTAAAG 57.412 47.619 0.00 0.00 0.00 1.85
845 877 4.312443 CTTTGCACTAAGACGGGACTAAA 58.688 43.478 0.00 0.00 0.00 1.85
868 907 1.260561 CGGGAAATCGATTTACGCCTG 59.739 52.381 23.50 19.98 42.26 4.85
881 920 2.043953 GGGCTGAAGGCGGGAAAT 60.044 61.111 0.00 0.00 42.94 2.17
914 955 5.303589 TGTTATCTTATCCGGGGAAGTAGTG 59.696 44.000 0.00 0.00 0.00 2.74
963 1004 1.671742 GAGGAGTTCGGGTTGCAGA 59.328 57.895 0.00 0.00 0.00 4.26
969 1010 1.689582 GGATGGGAGGAGTTCGGGT 60.690 63.158 0.00 0.00 0.00 5.28
971 1012 1.826024 CAGGATGGGAGGAGTTCGG 59.174 63.158 0.00 0.00 0.00 4.30
1017 1058 1.869824 AAGAGAGGGAGAGGAGCGGT 61.870 60.000 0.00 0.00 0.00 5.68
1221 1263 2.266055 GCTCCGAACCCACCTGAG 59.734 66.667 0.00 0.00 0.00 3.35
1254 1296 2.445654 CCCCTCCTCCTCAGCCTC 60.446 72.222 0.00 0.00 0.00 4.70
1258 1300 2.767496 CAGCCCCCTCCTCCTCAG 60.767 72.222 0.00 0.00 0.00 3.35
1442 1486 2.699954 AGTGGCAAACTTGACGGATAG 58.300 47.619 0.00 0.00 39.74 2.08
1444 1488 3.725754 AGTGGCAAACTTGACGGAT 57.274 47.368 0.00 0.00 39.74 4.18
1452 1496 4.370917 CAGTGCAAATTAAGTGGCAAACT 58.629 39.130 6.54 0.00 42.60 2.66
1453 1497 3.059665 GCAGTGCAAATTAAGTGGCAAAC 60.060 43.478 6.54 0.00 38.10 2.93
1454 1498 3.129871 GCAGTGCAAATTAAGTGGCAAA 58.870 40.909 6.54 0.00 38.10 3.68
1455 1499 2.364970 AGCAGTGCAAATTAAGTGGCAA 59.635 40.909 19.20 0.00 38.10 4.52
1456 1500 1.962807 AGCAGTGCAAATTAAGTGGCA 59.037 42.857 19.20 0.00 0.00 4.92
1458 1502 3.243839 ACCAAGCAGTGCAAATTAAGTGG 60.244 43.478 19.20 12.52 0.00 4.00
1459 1503 3.737266 CACCAAGCAGTGCAAATTAAGTG 59.263 43.478 19.20 10.44 0.00 3.16
1518 1587 2.026356 ACCCATACACAGCATTACAGCA 60.026 45.455 0.00 0.00 36.85 4.41
1519 1588 2.355756 CACCCATACACAGCATTACAGC 59.644 50.000 0.00 0.00 0.00 4.40
1520 1589 3.872696 TCACCCATACACAGCATTACAG 58.127 45.455 0.00 0.00 0.00 2.74
1521 1590 3.990959 TCACCCATACACAGCATTACA 57.009 42.857 0.00 0.00 0.00 2.41
1522 1591 5.835113 AATTCACCCATACACAGCATTAC 57.165 39.130 0.00 0.00 0.00 1.89
1523 1592 6.435591 TCAAAATTCACCCATACACAGCATTA 59.564 34.615 0.00 0.00 0.00 1.90
1524 1593 5.245751 TCAAAATTCACCCATACACAGCATT 59.754 36.000 0.00 0.00 0.00 3.56
1525 1594 4.771577 TCAAAATTCACCCATACACAGCAT 59.228 37.500 0.00 0.00 0.00 3.79
1539 1608 0.709992 CCCCCTCCCCTCAAAATTCA 59.290 55.000 0.00 0.00 0.00 2.57
1597 1666 9.528018 AGAAATCGACACACATTTTACAAAATT 57.472 25.926 0.00 0.00 36.52 1.82
1599 1668 7.646130 GGAGAAATCGACACACATTTTACAAAA 59.354 33.333 0.00 0.00 0.00 2.44
1616 1685 8.853345 CAAAATGTATTTCAAGTGGAGAAATCG 58.147 33.333 4.60 0.00 42.82 3.34
1618 1687 8.650490 ACCAAAATGTATTTCAAGTGGAGAAAT 58.350 29.630 10.99 6.43 45.05 2.17
1668 1737 6.814954 ATCCATCTACACTGACAATAAGGT 57.185 37.500 0.00 0.00 0.00 3.50
1727 1796 9.537192 CCAATTAACCACTCGTCTTATACAATA 57.463 33.333 0.00 0.00 0.00 1.90
1734 1803 7.225931 GCAATATCCAATTAACCACTCGTCTTA 59.774 37.037 0.00 0.00 0.00 2.10
1738 1807 5.189928 TGCAATATCCAATTAACCACTCGT 58.810 37.500 0.00 0.00 0.00 4.18
1745 1814 8.947055 AAATCCACTTGCAATATCCAATTAAC 57.053 30.769 0.00 0.00 0.00 2.01
1776 1845 4.081198 GGATGTTTTGTGGGCAATATTCCA 60.081 41.667 6.36 0.11 34.18 3.53
1803 1872 5.360429 GTGGTTTGTTACTTTTGTCCCCTTA 59.640 40.000 0.00 0.00 0.00 2.69
1813 1882 9.727859 AAACTAAATTTGGTGGTTTGTTACTTT 57.272 25.926 8.06 0.00 0.00 2.66
1846 1915 9.817809 GAACACCTATTATTCAGATGAAGTACA 57.182 33.333 1.32 0.00 37.48 2.90
1872 1941 7.912250 GCCATTAGATTTACTGAAATGACACAG 59.088 37.037 0.00 0.00 35.33 3.66
1892 1961 6.303839 GGAGGGAGTATTTTACATGCCATTA 58.696 40.000 0.00 0.00 0.00 1.90
1897 1966 3.805207 ACGGAGGGAGTATTTTACATGC 58.195 45.455 0.00 0.00 0.00 4.06
1901 1970 8.728337 ATAGAAAAACGGAGGGAGTATTTTAC 57.272 34.615 0.00 0.00 0.00 2.01
1908 1977 8.315220 TCTTATAATAGAAAAACGGAGGGAGT 57.685 34.615 0.00 0.00 0.00 3.85
1910 1979 8.711170 ACATCTTATAATAGAAAAACGGAGGGA 58.289 33.333 0.00 0.00 0.00 4.20
1911 1980 8.904099 ACATCTTATAATAGAAAAACGGAGGG 57.096 34.615 0.00 0.00 0.00 4.30
1930 1999 8.265055 TCTCTACGGAAATATCCAAAACATCTT 58.735 33.333 0.00 0.00 46.97 2.40
1932 2001 7.711339 AGTCTCTACGGAAATATCCAAAACATC 59.289 37.037 0.00 0.00 46.97 3.06
1934 2003 6.942976 AGTCTCTACGGAAATATCCAAAACA 58.057 36.000 0.00 0.00 46.97 2.83
1936 2005 8.070034 TGTAGTCTCTACGGAAATATCCAAAA 57.930 34.615 3.10 0.00 46.97 2.44
1937 2006 7.649533 TGTAGTCTCTACGGAAATATCCAAA 57.350 36.000 3.10 0.00 46.97 3.28
1939 2008 7.940688 TGTATGTAGTCTCTACGGAAATATCCA 59.059 37.037 3.10 0.00 46.97 3.41
1940 2009 8.332996 TGTATGTAGTCTCTACGGAAATATCC 57.667 38.462 3.10 0.00 42.80 2.59
1941 2010 9.217278 TCTGTATGTAGTCTCTACGGAAATATC 57.783 37.037 3.10 0.00 29.96 1.63
1942 2011 9.001542 GTCTGTATGTAGTCTCTACGGAAATAT 57.998 37.037 3.10 0.00 33.71 1.28
1943 2012 7.443575 GGTCTGTATGTAGTCTCTACGGAAATA 59.556 40.741 3.10 0.00 33.71 1.40
1944 2013 6.262720 GGTCTGTATGTAGTCTCTACGGAAAT 59.737 42.308 3.10 0.00 33.71 2.17
1945 2014 5.587844 GGTCTGTATGTAGTCTCTACGGAAA 59.412 44.000 3.10 0.00 33.71 3.13
1946 2015 5.121811 GGTCTGTATGTAGTCTCTACGGAA 58.878 45.833 3.10 0.00 33.71 4.30
1947 2016 4.162888 TGGTCTGTATGTAGTCTCTACGGA 59.837 45.833 3.10 0.00 0.00 4.69
1948 2017 4.449131 TGGTCTGTATGTAGTCTCTACGG 58.551 47.826 3.10 0.00 0.00 4.02
1949 2018 6.432607 TTTGGTCTGTATGTAGTCTCTACG 57.567 41.667 3.10 0.00 0.00 3.51
1950 2019 8.467598 TCATTTTGGTCTGTATGTAGTCTCTAC 58.532 37.037 0.59 0.59 0.00 2.59
1951 2020 8.589701 TCATTTTGGTCTGTATGTAGTCTCTA 57.410 34.615 0.00 0.00 0.00 2.43
1952 2021 7.179338 ACTCATTTTGGTCTGTATGTAGTCTCT 59.821 37.037 0.00 0.00 0.00 3.10
1953 2022 7.276658 CACTCATTTTGGTCTGTATGTAGTCTC 59.723 40.741 0.00 0.00 0.00 3.36
1954 2023 7.039011 TCACTCATTTTGGTCTGTATGTAGTCT 60.039 37.037 0.00 0.00 0.00 3.24
1955 2024 7.097192 TCACTCATTTTGGTCTGTATGTAGTC 58.903 38.462 0.00 0.00 0.00 2.59
1956 2025 7.004555 TCACTCATTTTGGTCTGTATGTAGT 57.995 36.000 0.00 0.00 0.00 2.73
1957 2026 7.387673 TGTTCACTCATTTTGGTCTGTATGTAG 59.612 37.037 0.00 0.00 0.00 2.74
1958 2027 7.220740 TGTTCACTCATTTTGGTCTGTATGTA 58.779 34.615 0.00 0.00 0.00 2.29
1959 2028 6.061441 TGTTCACTCATTTTGGTCTGTATGT 58.939 36.000 0.00 0.00 0.00 2.29
1960 2029 6.558771 TGTTCACTCATTTTGGTCTGTATG 57.441 37.500 0.00 0.00 0.00 2.39
1961 2030 7.068103 TGTTTGTTCACTCATTTTGGTCTGTAT 59.932 33.333 0.00 0.00 0.00 2.29
1962 2031 6.375736 TGTTTGTTCACTCATTTTGGTCTGTA 59.624 34.615 0.00 0.00 0.00 2.74
1963 2032 5.184864 TGTTTGTTCACTCATTTTGGTCTGT 59.815 36.000 0.00 0.00 0.00 3.41
1964 2033 5.516339 GTGTTTGTTCACTCATTTTGGTCTG 59.484 40.000 0.00 0.00 35.68 3.51
1965 2034 5.184864 TGTGTTTGTTCACTCATTTTGGTCT 59.815 36.000 0.00 0.00 38.90 3.85
1966 2035 5.288472 GTGTGTTTGTTCACTCATTTTGGTC 59.712 40.000 0.00 0.00 38.90 4.02
1967 2036 5.167845 GTGTGTTTGTTCACTCATTTTGGT 58.832 37.500 0.00 0.00 38.90 3.67
1968 2037 5.167121 TGTGTGTTTGTTCACTCATTTTGG 58.833 37.500 0.00 0.00 37.06 3.28
1969 2038 6.702972 TTGTGTGTTTGTTCACTCATTTTG 57.297 33.333 0.00 0.00 40.05 2.44
1970 2039 7.721286 TTTTGTGTGTTTGTTCACTCATTTT 57.279 28.000 0.00 0.00 40.05 1.82
1971 2040 7.721286 TTTTTGTGTGTTTGTTCACTCATTT 57.279 28.000 0.00 0.00 40.05 2.32
1972 2041 7.623925 GCATTTTTGTGTGTTTGTTCACTCATT 60.624 33.333 0.00 0.00 40.05 2.57
1973 2042 6.183360 GCATTTTTGTGTGTTTGTTCACTCAT 60.183 34.615 0.00 0.00 40.05 2.90
1974 2043 5.119898 GCATTTTTGTGTGTTTGTTCACTCA 59.880 36.000 0.00 0.00 39.13 3.41
1975 2044 5.550070 GCATTTTTGTGTGTTTGTTCACTC 58.450 37.500 0.00 0.00 38.90 3.51
1976 2045 4.091220 CGCATTTTTGTGTGTTTGTTCACT 59.909 37.500 0.00 0.00 38.90 3.41
1977 2046 4.143221 ACGCATTTTTGTGTGTTTGTTCAC 60.143 37.500 0.00 0.00 39.65 3.18
1978 2047 3.990469 ACGCATTTTTGTGTGTTTGTTCA 59.010 34.783 0.00 0.00 39.65 3.18
1979 2048 4.326009 AGACGCATTTTTGTGTGTTTGTTC 59.674 37.500 0.00 0.00 42.45 3.18
1980 2049 4.241681 AGACGCATTTTTGTGTGTTTGTT 58.758 34.783 0.00 0.00 42.45 2.83
1981 2050 3.843999 AGACGCATTTTTGTGTGTTTGT 58.156 36.364 0.00 0.00 42.45 2.83
1982 2051 7.795431 ATATAGACGCATTTTTGTGTGTTTG 57.205 32.000 0.00 0.00 42.45 2.93
1983 2052 8.508062 TGTATATAGACGCATTTTTGTGTGTTT 58.492 29.630 0.00 0.00 42.45 2.83
1984 2053 8.035165 TGTATATAGACGCATTTTTGTGTGTT 57.965 30.769 0.00 0.00 42.45 3.32
1985 2054 7.603963 TGTATATAGACGCATTTTTGTGTGT 57.396 32.000 0.00 0.00 44.85 3.72
1986 2055 7.798516 GGATGTATATAGACGCATTTTTGTGTG 59.201 37.037 0.00 0.00 35.76 3.82
1987 2056 7.497579 TGGATGTATATAGACGCATTTTTGTGT 59.502 33.333 0.00 0.00 34.95 3.72
1992 2061 9.283768 TGAATTGGATGTATATAGACGCATTTT 57.716 29.630 0.00 0.00 0.00 1.82
1997 2066 8.534333 TTCTTGAATTGGATGTATATAGACGC 57.466 34.615 0.00 0.00 0.00 5.19
2031 2100 8.926710 CCGTCCATTCACTATTATAAGATGTTC 58.073 37.037 0.00 0.00 0.00 3.18
2032 2101 8.647796 TCCGTCCATTCACTATTATAAGATGTT 58.352 33.333 0.00 0.00 0.00 2.71
2033 2102 8.190326 TCCGTCCATTCACTATTATAAGATGT 57.810 34.615 0.00 0.00 0.00 3.06
2034 2103 8.307483 ACTCCGTCCATTCACTATTATAAGATG 58.693 37.037 0.00 0.00 0.00 2.90
2035 2104 8.423906 ACTCCGTCCATTCACTATTATAAGAT 57.576 34.615 0.00 0.00 0.00 2.40
2037 2106 8.573885 TGTACTCCGTCCATTCACTATTATAAG 58.426 37.037 0.00 0.00 0.00 1.73
2038 2107 8.467963 TGTACTCCGTCCATTCACTATTATAA 57.532 34.615 0.00 0.00 0.00 0.98
2039 2108 8.467963 TTGTACTCCGTCCATTCACTATTATA 57.532 34.615 0.00 0.00 0.00 0.98
2040 2109 6.971726 TGTACTCCGTCCATTCACTATTAT 57.028 37.500 0.00 0.00 0.00 1.28
2041 2110 6.379133 ACTTGTACTCCGTCCATTCACTATTA 59.621 38.462 0.00 0.00 0.00 0.98
2044 2113 4.084287 ACTTGTACTCCGTCCATTCACTA 58.916 43.478 0.00 0.00 0.00 2.74
2045 2114 2.897969 ACTTGTACTCCGTCCATTCACT 59.102 45.455 0.00 0.00 0.00 3.41
2048 2117 4.809426 CCATAACTTGTACTCCGTCCATTC 59.191 45.833 0.00 0.00 0.00 2.67
2050 2119 3.134081 CCCATAACTTGTACTCCGTCCAT 59.866 47.826 0.00 0.00 0.00 3.41
2051 2120 2.498481 CCCATAACTTGTACTCCGTCCA 59.502 50.000 0.00 0.00 0.00 4.02
2055 2153 4.724074 TGTACCCATAACTTGTACTCCG 57.276 45.455 0.00 0.00 36.63 4.63
2063 2161 2.990998 ACCACCCTTGTACCCATAACTT 59.009 45.455 0.00 0.00 0.00 2.66
2064 2162 2.639487 ACCACCCTTGTACCCATAACT 58.361 47.619 0.00 0.00 0.00 2.24
2070 2168 2.041216 AGATGAAACCACCCTTGTACCC 59.959 50.000 0.00 0.00 0.00 3.69
2075 2173 1.270550 GTGCAGATGAAACCACCCTTG 59.729 52.381 0.00 0.00 0.00 3.61
2076 2174 1.133513 TGTGCAGATGAAACCACCCTT 60.134 47.619 0.00 0.00 0.00 3.95
2078 2176 1.327303 TTGTGCAGATGAAACCACCC 58.673 50.000 0.00 0.00 0.00 4.61
2080 2178 3.435105 TGTTTGTGCAGATGAAACCAC 57.565 42.857 0.00 0.00 0.00 4.16
2116 2215 4.708726 AACTTCTGGTATTGATTGCTGC 57.291 40.909 0.00 0.00 0.00 5.25
2117 2216 6.506500 AGAAACTTCTGGTATTGATTGCTG 57.493 37.500 0.00 0.00 35.89 4.41
2128 2227 9.152595 GATCTCGTATAAAAAGAAACTTCTGGT 57.847 33.333 0.00 0.00 37.65 4.00
2144 2244 4.921515 GCTTACGGCATTTGATCTCGTATA 59.078 41.667 0.00 0.00 41.35 1.47
2145 2245 3.741344 GCTTACGGCATTTGATCTCGTAT 59.259 43.478 0.00 0.00 41.35 3.06
2146 2246 3.120792 GCTTACGGCATTTGATCTCGTA 58.879 45.455 0.00 0.00 41.35 3.43
2147 2247 1.933853 GCTTACGGCATTTGATCTCGT 59.066 47.619 0.00 0.00 41.35 4.18
2148 2248 2.205074 AGCTTACGGCATTTGATCTCG 58.795 47.619 0.00 0.00 44.79 4.04
2153 2253 5.001232 AGAGTAAAAGCTTACGGCATTTGA 58.999 37.500 0.00 0.00 41.15 2.69
2211 2311 1.620323 GGTTGGGCATCAGCTTTCTTT 59.380 47.619 0.00 0.00 41.70 2.52
2220 2320 2.673775 TTTCTTCAGGTTGGGCATCA 57.326 45.000 0.00 0.00 0.00 3.07
2304 2404 1.682702 CCAGTATTCCTGTGCATGGCA 60.683 52.381 0.00 0.00 39.74 4.92
2328 2428 1.377725 AAGCCTGGACTTGCGATGG 60.378 57.895 0.00 0.00 0.00 3.51
2394 2494 0.607762 TTGCAGCAGGTTCGGCATTA 60.608 50.000 0.00 0.00 37.05 1.90
2400 2500 2.253452 GCAGTTGCAGCAGGTTCG 59.747 61.111 2.55 0.00 41.59 3.95
2413 2513 0.178873 TCCCCCAGAAACTAGGCAGT 60.179 55.000 0.00 0.00 36.19 4.40
2436 2536 2.410730 GCTGCTGCAAATTCACAATGAC 59.589 45.455 11.11 0.00 39.41 3.06
2441 2541 2.894763 AAAGCTGCTGCAAATTCACA 57.105 40.000 18.42 0.00 42.74 3.58
2444 2544 3.036075 AGGAAAAGCTGCTGCAAATTC 57.964 42.857 18.42 16.36 42.74 2.17
2447 2547 1.755959 TGAAGGAAAAGCTGCTGCAAA 59.244 42.857 18.42 0.00 42.74 3.68
2457 2557 4.219070 TGGCAAGATGTGATGAAGGAAAAG 59.781 41.667 0.00 0.00 0.00 2.27
2463 2563 5.350365 CCAAAATTGGCAAGATGTGATGAAG 59.650 40.000 5.96 0.00 42.21 3.02
2488 2588 6.593770 TGAGTTCGTTCAATAACATATGCTGT 59.406 34.615 1.58 0.00 40.84 4.40
2509 2609 2.826488 AGACCTGGCAGTCTATTGAGT 58.174 47.619 14.43 0.74 45.31 3.41
2557 2657 3.659786 AGCGAGCACATAAACACAGTAA 58.340 40.909 0.00 0.00 0.00 2.24
2575 2675 2.033927 TCAGAGCTTCTACTGCATAGCG 59.966 50.000 0.00 0.00 38.62 4.26
2581 2681 6.917217 ATATTGTTTCAGAGCTTCTACTGC 57.083 37.500 0.00 0.00 34.57 4.40
2582 2682 7.201679 CCCAATATTGTTTCAGAGCTTCTACTG 60.202 40.741 14.25 0.00 35.72 2.74
2583 2683 6.825721 CCCAATATTGTTTCAGAGCTTCTACT 59.174 38.462 14.25 0.00 0.00 2.57
2584 2684 6.458888 GCCCAATATTGTTTCAGAGCTTCTAC 60.459 42.308 14.25 0.00 0.00 2.59
2585 2685 5.590259 GCCCAATATTGTTTCAGAGCTTCTA 59.410 40.000 14.25 0.00 0.00 2.10
2586 2686 4.400567 GCCCAATATTGTTTCAGAGCTTCT 59.599 41.667 14.25 0.00 0.00 2.85
2587 2687 4.440663 GGCCCAATATTGTTTCAGAGCTTC 60.441 45.833 14.25 0.00 0.00 3.86
2588 2688 3.448660 GGCCCAATATTGTTTCAGAGCTT 59.551 43.478 14.25 0.00 0.00 3.74
2589 2689 3.026694 GGCCCAATATTGTTTCAGAGCT 58.973 45.455 14.25 0.00 0.00 4.09
2596 2696 4.263418 ACAAGCAATGGCCCAATATTGTTT 60.263 37.500 14.25 11.22 42.56 2.83
2597 2697 3.263937 ACAAGCAATGGCCCAATATTGTT 59.736 39.130 14.25 6.29 42.56 2.83
2601 2701 3.036452 AGACAAGCAATGGCCCAATAT 57.964 42.857 0.00 0.00 38.06 1.28
2602 2702 2.530460 AGACAAGCAATGGCCCAATA 57.470 45.000 0.00 0.00 38.06 1.90
2655 2755 7.016170 TCTGCATACACCATACAACAGGTATAT 59.984 37.037 0.00 0.00 40.76 0.86
2663 2763 7.657354 TGAAGATATCTGCATACACCATACAAC 59.343 37.037 9.55 0.00 0.00 3.32
2713 2813 5.739959 AGAAGGTAAGGAGAGAAAGCATTC 58.260 41.667 0.00 0.00 35.70 2.67
2717 2817 3.118555 GGGAGAAGGTAAGGAGAGAAAGC 60.119 52.174 0.00 0.00 0.00 3.51
2727 2827 6.199937 CATTTCACAATGGGAGAAGGTAAG 57.800 41.667 0.00 0.00 36.82 2.34
2768 2868 8.774586 TCTCATTAGAGTACAAAAGAAAACAGC 58.225 33.333 0.00 0.00 42.66 4.40
2787 2887 5.943349 TCCAGGGTCGTATTTTCTCATTA 57.057 39.130 0.00 0.00 0.00 1.90
2833 2938 3.041211 ACAGGCCTAGAGCAATACATCA 58.959 45.455 3.98 0.00 46.50 3.07
2970 3075 1.722851 AGAGGAGGGTCAAGGTAGGAA 59.277 52.381 0.00 0.00 0.00 3.36
2972 3077 1.273324 ACAGAGGAGGGTCAAGGTAGG 60.273 57.143 0.00 0.00 0.00 3.18
2974 3079 2.715763 AACAGAGGAGGGTCAAGGTA 57.284 50.000 0.00 0.00 0.00 3.08
2975 3080 1.821088 AAACAGAGGAGGGTCAAGGT 58.179 50.000 0.00 0.00 0.00 3.50
2976 3081 2.959465 AAAACAGAGGAGGGTCAAGG 57.041 50.000 0.00 0.00 0.00 3.61
2978 3083 5.118729 TGTTTAAAACAGAGGAGGGTCAA 57.881 39.130 0.00 0.00 36.25 3.18
3061 3166 4.162131 GGGTACGGTTACAATCCTCCTAAA 59.838 45.833 0.00 0.00 0.00 1.85
3062 3167 3.706086 GGGTACGGTTACAATCCTCCTAA 59.294 47.826 0.00 0.00 0.00 2.69
3094 3199 3.059166 ACCTTTGCGTTTCATTGCATTC 58.941 40.909 0.00 0.00 41.42 2.67
3147 3252 4.214332 CAGGTTGCTCCAGTTAAGAGAAAC 59.786 45.833 5.77 5.77 45.62 2.78
3192 3297 2.160065 ACGAGAACGCGTTGAAATTACG 60.160 45.455 31.89 22.30 42.71 3.18


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

AutoCloner maintained by Alex Coulton.