Multiple sequence alignment - TraesCS3A01G459300

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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 TraesCS3A01G459300 chr3A 100.000 2447 0 0 1 2447 695755725 695753279 0.000000e+00 4519.0
1 TraesCS3A01G459300 chr3A 91.296 1080 82 7 371 1449 695745693 695744625 0.000000e+00 1463.0
2 TraesCS3A01G459300 chr3A 85.261 1228 146 16 404 1604 695668482 695669701 0.000000e+00 1232.0
3 TraesCS3A01G459300 chr3D 94.760 2023 73 10 1 2021 559228650 559226659 0.000000e+00 3118.0
4 TraesCS3A01G459300 chr3D 89.239 1366 108 20 387 1722 559219747 559218391 0.000000e+00 1672.0
5 TraesCS3A01G459300 chr3D 87.554 1165 122 12 404 1552 559162579 559163736 0.000000e+00 1327.0
6 TraesCS3A01G459300 chr3D 83.233 1163 154 21 404 1552 559165372 559166507 0.000000e+00 1029.0
7 TraesCS3A01G459300 chr3D 95.402 174 8 0 2137 2310 559226659 559226486 6.660000e-71 278.0
8 TraesCS3A01G459300 chr3D 97.436 39 1 0 240 278 559162433 559162471 1.570000e-07 67.6
9 TraesCS3A01G459300 chr3B 86.943 1593 141 34 90 1648 742256770 742255211 0.000000e+00 1727.0
10 TraesCS3A01G459300 chr3B 91.272 1203 83 10 402 1604 742476770 742477950 0.000000e+00 1620.0
11 TraesCS3A01G459300 chr3B 81.380 1246 180 33 370 1603 742163685 742164890 0.000000e+00 968.0
12 TraesCS3A01G459300 chr3B 100.000 37 0 0 2311 2347 126000392 126000356 4.370000e-08 69.4
13 TraesCS3A01G459300 chr7A 93.407 91 3 3 2311 2398 134028791 134028701 5.490000e-27 132.0
14 TraesCS3A01G459300 chr7A 86.747 83 10 1 1690 1771 577198392 577198474 9.320000e-15 91.6
15 TraesCS3A01G459300 chr4B 95.181 83 4 0 2313 2395 82571305 82571387 5.490000e-27 132.0
16 TraesCS3A01G459300 chr5A 95.000 80 4 0 2312 2391 598001892 598001971 2.550000e-25 126.0
17 TraesCS3A01G459300 chr5B 93.750 80 5 0 2312 2391 587059945 587060024 1.190000e-23 121.0
18 TraesCS3A01G459300 chr5B 97.917 48 1 0 2399 2446 602261530 602261577 1.560000e-12 84.2
19 TraesCS3A01G459300 chr7D 94.643 56 1 2 2392 2446 606945795 606945741 4.340000e-13 86.1
20 TraesCS3A01G459300 chr7D 94.118 51 3 0 2395 2445 84324415 84324465 7.250000e-11 78.7
21 TraesCS3A01G459300 chr7B 97.872 47 1 0 2399 2445 482080607 482080561 5.610000e-12 82.4
22 TraesCS3A01G459300 chr6B 92.727 55 4 0 2393 2447 21011816 21011870 2.020000e-11 80.5
23 TraesCS3A01G459300 chr1B 95.918 49 2 0 2398 2446 574254956 574255004 2.020000e-11 80.5
24 TraesCS3A01G459300 chr1B 95.833 48 2 0 2399 2446 574256322 574256275 7.250000e-11 78.7
25 TraesCS3A01G459300 chr2A 95.833 48 2 0 2399 2446 759737576 759737623 7.250000e-11 78.7
26 TraesCS3A01G459300 chr6D 95.745 47 2 0 2399 2445 68056926 68056972 2.610000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G459300 chr3A 695753279 695755725 2446 True 4519.000000 4519 100.000000 1 2447 1 chr3A.!!$R2 2446
1 TraesCS3A01G459300 chr3A 695744625 695745693 1068 True 1463.000000 1463 91.296000 371 1449 1 chr3A.!!$R1 1078
2 TraesCS3A01G459300 chr3A 695668482 695669701 1219 False 1232.000000 1232 85.261000 404 1604 1 chr3A.!!$F1 1200
3 TraesCS3A01G459300 chr3D 559226486 559228650 2164 True 1698.000000 3118 95.081000 1 2310 2 chr3D.!!$R2 2309
4 TraesCS3A01G459300 chr3D 559218391 559219747 1356 True 1672.000000 1672 89.239000 387 1722 1 chr3D.!!$R1 1335
5 TraesCS3A01G459300 chr3D 559162433 559166507 4074 False 807.866667 1327 89.407667 240 1552 3 chr3D.!!$F1 1312
6 TraesCS3A01G459300 chr3B 742255211 742256770 1559 True 1727.000000 1727 86.943000 90 1648 1 chr3B.!!$R2 1558
7 TraesCS3A01G459300 chr3B 742476770 742477950 1180 False 1620.000000 1620 91.272000 402 1604 1 chr3B.!!$F2 1202
8 TraesCS3A01G459300 chr3B 742163685 742164890 1205 False 968.000000 968 81.380000 370 1603 1 chr3B.!!$F1 1233

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
158 159 0.525761 CGTCCATTTGGTGCCGATTT 59.474 50.0 0.0 0.0 36.34 2.17 F
1062 1106 0.107897 TGTCGCACAACAACCTCACT 60.108 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1245 1.134367 CACGCCTGAGAGGTCGAAATA 59.866 52.381 11.66 0.00 37.80 1.40 R
2371 5241 0.526211 CCTGATGAGGTCGTCGAACA 59.474 55.000 13.74 6.76 34.16 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
51 52 1.871039 GTTAGAAAGGCAGCGTGTTGA 59.129 47.619 0.00 0.00 0.00 3.18
61 62 2.396601 CAGCGTGTTGAACAATTGCAT 58.603 42.857 16.99 0.00 0.00 3.96
62 63 2.154198 CAGCGTGTTGAACAATTGCATG 59.846 45.455 16.99 1.73 0.00 4.06
63 64 2.034432 AGCGTGTTGAACAATTGCATGA 59.966 40.909 16.99 0.00 0.00 3.07
64 65 2.793790 GCGTGTTGAACAATTGCATGAA 59.206 40.909 5.05 0.00 0.00 2.57
65 66 3.429543 GCGTGTTGAACAATTGCATGAAT 59.570 39.130 5.05 0.00 0.00 2.57
66 67 4.084433 GCGTGTTGAACAATTGCATGAATT 60.084 37.500 5.05 0.00 34.34 2.17
67 68 5.558653 GCGTGTTGAACAATTGCATGAATTT 60.559 36.000 5.05 0.00 31.41 1.82
68 69 6.420588 CGTGTTGAACAATTGCATGAATTTT 58.579 32.000 5.05 0.00 31.41 1.82
69 70 6.906143 CGTGTTGAACAATTGCATGAATTTTT 59.094 30.769 5.05 0.00 31.41 1.94
158 159 0.525761 CGTCCATTTGGTGCCGATTT 59.474 50.000 0.00 0.00 36.34 2.17
234 245 9.797642 ATTATATGCACCTTATTCTTGATGTGA 57.202 29.630 0.00 0.00 0.00 3.58
235 246 9.797642 TTATATGCACCTTATTCTTGATGTGAT 57.202 29.630 0.00 0.00 0.00 3.06
237 248 4.883585 TGCACCTTATTCTTGATGTGATCC 59.116 41.667 0.00 0.00 0.00 3.36
238 249 4.883585 GCACCTTATTCTTGATGTGATCCA 59.116 41.667 0.00 0.00 0.00 3.41
506 547 2.683933 GAGCCCTCTCCGGAACCA 60.684 66.667 5.23 0.00 33.19 3.67
595 636 1.134367 CTATGACTTCGCGTCCTGGAA 59.866 52.381 5.77 0.00 42.13 3.53
623 664 2.185350 CCCTGCTGCGACTGGTAG 59.815 66.667 0.00 0.00 0.00 3.18
905 946 3.053991 TCCTCGATCTCTCCTTCAACTCT 60.054 47.826 0.00 0.00 0.00 3.24
952 993 1.526917 GGACCATCCCCAATCTGCG 60.527 63.158 0.00 0.00 0.00 5.18
1062 1106 0.107897 TGTCGCACAACAACCTCACT 60.108 50.000 0.00 0.00 0.00 3.41
1085 1129 2.202932 CATCCCGGCAGACTTCGG 60.203 66.667 0.00 6.95 45.29 4.30
1195 1239 2.579657 ATCGACCTGTCCCGCAACA 61.580 57.895 0.00 0.00 0.00 3.33
1201 1245 1.071471 CTGTCCCGCAACACCTTCT 59.929 57.895 0.00 0.00 0.00 2.85
1272 1319 0.251698 TGAGCCACAATGCCATCCAA 60.252 50.000 0.00 0.00 0.00 3.53
1534 4394 3.744214 CGCCCTGGAATAAGAGTTATGCA 60.744 47.826 0.00 0.00 0.00 3.96
1681 4551 8.721133 ACCAAAGTCAGGTTAATTTCCTTTAT 57.279 30.769 0.00 0.00 35.33 1.40
1805 4675 2.751166 AGAAGGACAGTCGTTGGATG 57.249 50.000 13.23 0.00 0.00 3.51
1806 4676 1.971357 AGAAGGACAGTCGTTGGATGT 59.029 47.619 13.23 0.00 0.00 3.06
1807 4677 2.368875 AGAAGGACAGTCGTTGGATGTT 59.631 45.455 13.23 0.00 0.00 2.71
1808 4678 2.169832 AGGACAGTCGTTGGATGTTG 57.830 50.000 0.00 0.00 0.00 3.33
1809 4679 1.416401 AGGACAGTCGTTGGATGTTGT 59.584 47.619 0.00 0.00 0.00 3.32
1810 4680 2.631062 AGGACAGTCGTTGGATGTTGTA 59.369 45.455 0.00 0.00 0.00 2.41
1811 4681 3.260884 AGGACAGTCGTTGGATGTTGTAT 59.739 43.478 0.00 0.00 0.00 2.29
1841 4711 0.250770 AGGCCCAGAAAACCGACTTC 60.251 55.000 0.00 0.00 0.00 3.01
1869 4739 9.672086 CCAAAATTAATTTTCAGACGACTTACA 57.328 29.630 20.71 0.00 37.86 2.41
1962 4832 9.534565 CATTTCAATTCTTCTATACTTCTCCGA 57.465 33.333 0.00 0.00 0.00 4.55
2020 4890 0.913934 TGCAGTCATGGCCCCTTAGA 60.914 55.000 0.00 0.00 0.00 2.10
2021 4891 0.475906 GCAGTCATGGCCCCTTAGAT 59.524 55.000 0.00 0.00 0.00 1.98
2022 4892 1.816961 GCAGTCATGGCCCCTTAGATG 60.817 57.143 0.00 0.00 0.00 2.90
2023 4893 1.143813 AGTCATGGCCCCTTAGATGG 58.856 55.000 0.00 0.00 0.00 3.51
2024 4894 0.846693 GTCATGGCCCCTTAGATGGT 59.153 55.000 0.00 0.00 0.00 3.55
2025 4895 1.215423 GTCATGGCCCCTTAGATGGTT 59.785 52.381 0.00 0.00 0.00 3.67
2026 4896 1.929494 TCATGGCCCCTTAGATGGTTT 59.071 47.619 0.00 0.00 0.00 3.27
2027 4897 2.314549 TCATGGCCCCTTAGATGGTTTT 59.685 45.455 0.00 0.00 0.00 2.43
2028 4898 3.106827 CATGGCCCCTTAGATGGTTTTT 58.893 45.455 0.00 0.00 0.00 1.94
2029 4899 4.017037 TCATGGCCCCTTAGATGGTTTTTA 60.017 41.667 0.00 0.00 0.00 1.52
2030 4900 4.618378 TGGCCCCTTAGATGGTTTTTAT 57.382 40.909 0.00 0.00 0.00 1.40
2031 4901 4.542697 TGGCCCCTTAGATGGTTTTTATC 58.457 43.478 0.00 0.00 0.00 1.75
2032 4902 3.568430 GGCCCCTTAGATGGTTTTTATCG 59.432 47.826 0.00 0.00 0.00 2.92
2033 4903 3.004419 GCCCCTTAGATGGTTTTTATCGC 59.996 47.826 0.00 0.00 0.00 4.58
2034 4904 3.568430 CCCCTTAGATGGTTTTTATCGCC 59.432 47.826 0.00 0.00 0.00 5.54
2035 4905 3.568430 CCCTTAGATGGTTTTTATCGCCC 59.432 47.826 0.00 0.00 0.00 6.13
2036 4906 4.461198 CCTTAGATGGTTTTTATCGCCCT 58.539 43.478 0.00 0.00 0.00 5.19
2037 4907 4.515567 CCTTAGATGGTTTTTATCGCCCTC 59.484 45.833 0.00 0.00 0.00 4.30
2038 4908 3.933861 AGATGGTTTTTATCGCCCTCT 57.066 42.857 0.00 0.00 0.00 3.69
2039 4909 3.545703 AGATGGTTTTTATCGCCCTCTG 58.454 45.455 0.00 0.00 0.00 3.35
2040 4910 3.199946 AGATGGTTTTTATCGCCCTCTGA 59.800 43.478 0.00 0.00 0.00 3.27
2041 4911 3.644966 TGGTTTTTATCGCCCTCTGAT 57.355 42.857 0.00 0.00 0.00 2.90
2042 4912 3.541632 TGGTTTTTATCGCCCTCTGATC 58.458 45.455 0.00 0.00 0.00 2.92
2043 4913 3.054728 TGGTTTTTATCGCCCTCTGATCA 60.055 43.478 0.00 0.00 0.00 2.92
2044 4914 3.945285 GGTTTTTATCGCCCTCTGATCAA 59.055 43.478 0.00 0.00 0.00 2.57
2045 4915 4.398044 GGTTTTTATCGCCCTCTGATCAAA 59.602 41.667 0.00 0.00 0.00 2.69
2046 4916 5.105917 GGTTTTTATCGCCCTCTGATCAAAA 60.106 40.000 0.00 0.00 30.55 2.44
2047 4917 6.405842 GGTTTTTATCGCCCTCTGATCAAAAT 60.406 38.462 0.00 0.00 33.79 1.82
2048 4918 6.377327 TTTTATCGCCCTCTGATCAAAATC 57.623 37.500 0.00 0.00 0.00 2.17
2049 4919 1.939974 TCGCCCTCTGATCAAAATCG 58.060 50.000 0.00 0.00 34.39 3.34
2050 4920 1.480545 TCGCCCTCTGATCAAAATCGA 59.519 47.619 0.00 0.00 34.39 3.59
2051 4921 2.093711 TCGCCCTCTGATCAAAATCGAA 60.094 45.455 0.00 0.00 34.39 3.71
2052 4922 2.030946 CGCCCTCTGATCAAAATCGAAC 59.969 50.000 0.00 0.00 34.39 3.95
2053 4923 3.009723 GCCCTCTGATCAAAATCGAACA 58.990 45.455 0.00 0.00 34.39 3.18
2054 4924 3.629398 GCCCTCTGATCAAAATCGAACAT 59.371 43.478 0.00 0.00 34.39 2.71
2055 4925 4.096984 GCCCTCTGATCAAAATCGAACATT 59.903 41.667 0.00 0.00 34.39 2.71
2056 4926 5.296780 GCCCTCTGATCAAAATCGAACATTA 59.703 40.000 0.00 0.00 34.39 1.90
2057 4927 6.183360 GCCCTCTGATCAAAATCGAACATTAA 60.183 38.462 0.00 0.00 34.39 1.40
2058 4928 7.469181 GCCCTCTGATCAAAATCGAACATTAAT 60.469 37.037 0.00 0.00 34.39 1.40
2059 4929 8.072567 CCCTCTGATCAAAATCGAACATTAATC 58.927 37.037 0.00 0.00 34.39 1.75
2060 4930 8.834465 CCTCTGATCAAAATCGAACATTAATCT 58.166 33.333 0.00 0.00 34.39 2.40
2065 4935 9.784824 GATCAAAATCGAACATTAATCTAGTCG 57.215 33.333 0.00 0.00 0.00 4.18
2066 4936 8.920509 TCAAAATCGAACATTAATCTAGTCGA 57.079 30.769 10.13 10.13 0.00 4.20
2067 4937 9.529325 TCAAAATCGAACATTAATCTAGTCGAT 57.471 29.630 12.74 12.74 40.17 3.59
2071 4941 9.613957 AATCGAACATTAATCTAGTCGATAGTG 57.386 33.333 16.37 1.37 37.98 2.74
2072 4942 8.374327 TCGAACATTAATCTAGTCGATAGTGA 57.626 34.615 0.00 0.00 32.85 3.41
2073 4943 8.281194 TCGAACATTAATCTAGTCGATAGTGAC 58.719 37.037 0.00 0.00 39.21 3.67
2074 4944 8.068380 CGAACATTAATCTAGTCGATAGTGACA 58.932 37.037 0.00 0.00 41.41 3.58
2075 4945 9.900710 GAACATTAATCTAGTCGATAGTGACAT 57.099 33.333 0.00 0.00 41.41 3.06
2080 4950 9.774413 TTAATCTAGTCGATAGTGACATACTCA 57.226 33.333 0.00 0.00 41.41 3.41
2081 4951 7.899178 ATCTAGTCGATAGTGACATACTCAG 57.101 40.000 0.00 0.00 41.41 3.35
2082 4952 7.052142 TCTAGTCGATAGTGACATACTCAGA 57.948 40.000 0.00 0.00 41.41 3.27
2083 4953 5.994887 AGTCGATAGTGACATACTCAGAC 57.005 43.478 0.00 0.00 41.41 3.51
2084 4954 4.817464 AGTCGATAGTGACATACTCAGACC 59.183 45.833 0.00 0.00 41.41 3.85
2085 4955 4.023878 GTCGATAGTGACATACTCAGACCC 60.024 50.000 0.00 0.00 40.89 4.46
2086 4956 4.138290 CGATAGTGACATACTCAGACCCT 58.862 47.826 0.00 0.00 40.89 4.34
2087 4957 4.580995 CGATAGTGACATACTCAGACCCTT 59.419 45.833 0.00 0.00 40.89 3.95
2088 4958 5.278071 CGATAGTGACATACTCAGACCCTTC 60.278 48.000 0.00 0.00 40.89 3.46
2089 4959 4.054359 AGTGACATACTCAGACCCTTCT 57.946 45.455 0.00 0.00 33.17 2.85
2090 4960 4.421131 AGTGACATACTCAGACCCTTCTT 58.579 43.478 0.00 0.00 33.17 2.52
2091 4961 4.841246 AGTGACATACTCAGACCCTTCTTT 59.159 41.667 0.00 0.00 33.17 2.52
2092 4962 5.046950 AGTGACATACTCAGACCCTTCTTTC 60.047 44.000 0.00 0.00 33.17 2.62
2093 4963 4.223032 TGACATACTCAGACCCTTCTTTCC 59.777 45.833 0.00 0.00 0.00 3.13
2094 4964 4.168101 ACATACTCAGACCCTTCTTTCCA 58.832 43.478 0.00 0.00 0.00 3.53
2095 4965 4.597507 ACATACTCAGACCCTTCTTTCCAA 59.402 41.667 0.00 0.00 0.00 3.53
2096 4966 5.073144 ACATACTCAGACCCTTCTTTCCAAA 59.927 40.000 0.00 0.00 0.00 3.28
2097 4967 4.731313 ACTCAGACCCTTCTTTCCAAAT 57.269 40.909 0.00 0.00 0.00 2.32
2098 4968 4.401925 ACTCAGACCCTTCTTTCCAAATG 58.598 43.478 0.00 0.00 0.00 2.32
2099 4969 4.104738 ACTCAGACCCTTCTTTCCAAATGA 59.895 41.667 0.00 0.00 0.00 2.57
2100 4970 4.655963 TCAGACCCTTCTTTCCAAATGAG 58.344 43.478 0.00 0.00 0.00 2.90
2101 4971 4.350816 TCAGACCCTTCTTTCCAAATGAGA 59.649 41.667 0.00 0.00 0.00 3.27
2102 4972 5.072741 CAGACCCTTCTTTCCAAATGAGAA 58.927 41.667 0.00 0.00 0.00 2.87
2103 4973 5.048434 CAGACCCTTCTTTCCAAATGAGAAC 60.048 44.000 0.00 0.00 0.00 3.01
2104 4974 4.152647 ACCCTTCTTTCCAAATGAGAACC 58.847 43.478 0.00 0.00 0.00 3.62
2105 4975 4.151883 CCCTTCTTTCCAAATGAGAACCA 58.848 43.478 0.00 0.00 0.00 3.67
2106 4976 4.774200 CCCTTCTTTCCAAATGAGAACCAT 59.226 41.667 0.00 0.00 36.99 3.55
2107 4977 5.951747 CCCTTCTTTCCAAATGAGAACCATA 59.048 40.000 0.00 0.00 34.45 2.74
2108 4978 6.608808 CCCTTCTTTCCAAATGAGAACCATAT 59.391 38.462 0.00 0.00 34.45 1.78
2109 4979 7.124750 CCCTTCTTTCCAAATGAGAACCATATT 59.875 37.037 0.00 0.00 34.45 1.28
2110 4980 8.193438 CCTTCTTTCCAAATGAGAACCATATTC 58.807 37.037 0.00 0.00 34.45 1.75
2111 4981 8.884124 TTCTTTCCAAATGAGAACCATATTCT 57.116 30.769 0.00 0.00 34.45 2.40
2112 4982 8.884124 TCTTTCCAAATGAGAACCATATTCTT 57.116 30.769 0.00 0.00 34.45 2.52
2113 4983 9.312904 TCTTTCCAAATGAGAACCATATTCTTT 57.687 29.630 0.00 0.00 34.45 2.52
2114 4984 9.933723 CTTTCCAAATGAGAACCATATTCTTTT 57.066 29.630 0.00 0.00 34.45 2.27
2134 5004 4.473477 TTTTTCCCGCAAAAGAAAGGAA 57.527 36.364 0.00 0.00 35.34 3.36
2135 5005 4.473477 TTTTCCCGCAAAAGAAAGGAAA 57.527 36.364 0.00 0.00 43.14 3.13
2171 5041 3.266510 AGTGCCATCGTCAATACACAT 57.733 42.857 0.00 0.00 0.00 3.21
2213 5083 7.819415 TCATGAGACTACAAACAAGGTGATAAG 59.181 37.037 0.00 0.00 0.00 1.73
2253 5123 1.762957 AGATATGTACAAGTGCCCGCT 59.237 47.619 0.00 0.00 0.00 5.52
2282 5152 1.410517 TCTTTTCCCAAATGCACGCAA 59.589 42.857 0.00 0.00 0.00 4.85
2292 5162 0.806868 ATGCACGCAACCTTGATCAG 59.193 50.000 0.00 0.00 0.00 2.90
2310 5180 6.542821 TGATCAGTCCTTTCTATGGTTGTTT 58.457 36.000 0.00 0.00 0.00 2.83
2311 5181 7.004086 TGATCAGTCCTTTCTATGGTTGTTTT 58.996 34.615 0.00 0.00 0.00 2.43
2312 5182 7.505585 TGATCAGTCCTTTCTATGGTTGTTTTT 59.494 33.333 0.00 0.00 0.00 1.94
2334 5204 4.674281 TTTTTGCGGGGAAATACTTTGT 57.326 36.364 0.00 0.00 0.00 2.83
2335 5205 5.786264 TTTTTGCGGGGAAATACTTTGTA 57.214 34.783 0.00 0.00 0.00 2.41
2336 5206 5.986501 TTTTGCGGGGAAATACTTTGTAT 57.013 34.783 0.00 0.00 0.00 2.29
2337 5207 5.986501 TTTGCGGGGAAATACTTTGTATT 57.013 34.783 0.00 0.00 0.00 1.89
2338 5208 7.463961 TTTTGCGGGGAAATACTTTGTATTA 57.536 32.000 3.76 0.00 0.00 0.98
2339 5209 6.439675 TTGCGGGGAAATACTTTGTATTAC 57.560 37.500 3.76 1.51 0.00 1.89
2340 5210 5.747342 TGCGGGGAAATACTTTGTATTACT 58.253 37.500 3.76 0.00 0.00 2.24
2341 5211 5.818857 TGCGGGGAAATACTTTGTATTACTC 59.181 40.000 3.76 0.17 0.00 2.59
2342 5212 5.818857 GCGGGGAAATACTTTGTATTACTCA 59.181 40.000 3.76 0.00 0.00 3.41
2343 5213 6.316890 GCGGGGAAATACTTTGTATTACTCAA 59.683 38.462 3.76 0.00 0.00 3.02
2344 5214 7.148205 GCGGGGAAATACTTTGTATTACTCAAA 60.148 37.037 3.76 0.00 34.34 2.69
2345 5215 8.899771 CGGGGAAATACTTTGTATTACTCAAAT 58.100 33.333 3.76 0.00 34.88 2.32
2364 5234 8.812972 ACTCAAATAGTAGGATTACACTCAACA 58.187 33.333 0.00 0.00 36.36 3.33
2365 5235 9.823647 CTCAAATAGTAGGATTACACTCAACAT 57.176 33.333 0.00 0.00 31.96 2.71
2366 5236 9.599866 TCAAATAGTAGGATTACACTCAACATG 57.400 33.333 0.00 0.00 31.96 3.21
2367 5237 9.599866 CAAATAGTAGGATTACACTCAACATGA 57.400 33.333 0.00 0.00 31.96 3.07
2368 5238 9.601217 AAATAGTAGGATTACACTCAACATGAC 57.399 33.333 0.00 0.00 31.96 3.06
2369 5239 6.605471 AGTAGGATTACACTCAACATGACA 57.395 37.500 0.00 0.00 31.96 3.58
2370 5240 7.187824 AGTAGGATTACACTCAACATGACAT 57.812 36.000 0.00 0.00 31.96 3.06
2371 5241 7.624549 AGTAGGATTACACTCAACATGACATT 58.375 34.615 0.00 0.00 31.96 2.71
2372 5242 6.748333 AGGATTACACTCAACATGACATTG 57.252 37.500 0.00 0.00 0.00 2.82
2373 5243 6.240894 AGGATTACACTCAACATGACATTGT 58.759 36.000 0.00 0.00 0.00 2.71
2374 5244 6.716628 AGGATTACACTCAACATGACATTGTT 59.283 34.615 0.00 0.00 40.39 2.83
2375 5245 7.023575 GGATTACACTCAACATGACATTGTTC 58.976 38.462 0.00 0.00 37.73 3.18
2376 5246 4.472691 ACACTCAACATGACATTGTTCG 57.527 40.909 0.00 0.00 37.73 3.95
2377 5247 4.126437 ACACTCAACATGACATTGTTCGA 58.874 39.130 0.00 0.00 37.73 3.71
2378 5248 4.024893 ACACTCAACATGACATTGTTCGAC 60.025 41.667 0.00 0.00 37.73 4.20
2379 5249 3.184379 ACTCAACATGACATTGTTCGACG 59.816 43.478 0.00 0.00 37.73 5.12
2380 5250 3.385577 TCAACATGACATTGTTCGACGA 58.614 40.909 0.00 0.00 37.73 4.20
2381 5251 3.183574 TCAACATGACATTGTTCGACGAC 59.816 43.478 0.00 0.00 37.73 4.34
2382 5252 2.066262 ACATGACATTGTTCGACGACC 58.934 47.619 0.00 0.00 0.00 4.79
2383 5253 2.288825 ACATGACATTGTTCGACGACCT 60.289 45.455 0.00 0.00 0.00 3.85
2384 5254 2.060326 TGACATTGTTCGACGACCTC 57.940 50.000 0.00 0.00 0.00 3.85
2385 5255 1.338655 TGACATTGTTCGACGACCTCA 59.661 47.619 0.00 0.00 0.00 3.86
2386 5256 2.029380 TGACATTGTTCGACGACCTCAT 60.029 45.455 0.00 0.00 0.00 2.90
2387 5257 2.599082 GACATTGTTCGACGACCTCATC 59.401 50.000 0.00 0.00 0.00 2.92
2388 5258 2.029380 ACATTGTTCGACGACCTCATCA 60.029 45.455 0.00 0.00 0.00 3.07
2389 5259 2.347697 TTGTTCGACGACCTCATCAG 57.652 50.000 0.00 0.00 0.00 2.90
2390 5260 0.526211 TGTTCGACGACCTCATCAGG 59.474 55.000 0.00 0.00 46.87 3.86
2409 5279 6.235231 TCAGGTCCTGATGAGTTATTTACC 57.765 41.667 18.15 0.00 35.39 2.85
2410 5280 5.130477 TCAGGTCCTGATGAGTTATTTACCC 59.870 44.000 18.15 0.00 35.39 3.69
2411 5281 5.036916 AGGTCCTGATGAGTTATTTACCCA 58.963 41.667 0.00 0.00 0.00 4.51
2412 5282 5.491078 AGGTCCTGATGAGTTATTTACCCAA 59.509 40.000 0.00 0.00 0.00 4.12
2413 5283 6.011981 AGGTCCTGATGAGTTATTTACCCAAA 60.012 38.462 0.00 0.00 0.00 3.28
2414 5284 6.661805 GGTCCTGATGAGTTATTTACCCAAAA 59.338 38.462 0.00 0.00 0.00 2.44
2415 5285 7.362660 GGTCCTGATGAGTTATTTACCCAAAAC 60.363 40.741 0.00 0.00 0.00 2.43
2416 5286 6.661805 TCCTGATGAGTTATTTACCCAAAACC 59.338 38.462 0.00 0.00 0.00 3.27
2417 5287 6.435904 CCTGATGAGTTATTTACCCAAAACCA 59.564 38.462 0.00 0.00 0.00 3.67
2418 5288 7.222000 TGATGAGTTATTTACCCAAAACCAC 57.778 36.000 0.00 0.00 0.00 4.16
2419 5289 6.209788 TGATGAGTTATTTACCCAAAACCACC 59.790 38.462 0.00 0.00 0.00 4.61
2420 5290 5.455872 TGAGTTATTTACCCAAAACCACCA 58.544 37.500 0.00 0.00 0.00 4.17
2421 5291 5.302313 TGAGTTATTTACCCAAAACCACCAC 59.698 40.000 0.00 0.00 0.00 4.16
2422 5292 5.209659 AGTTATTTACCCAAAACCACCACA 58.790 37.500 0.00 0.00 0.00 4.17
2423 5293 5.841783 AGTTATTTACCCAAAACCACCACAT 59.158 36.000 0.00 0.00 0.00 3.21
2424 5294 6.327887 AGTTATTTACCCAAAACCACCACATT 59.672 34.615 0.00 0.00 0.00 2.71
2425 5295 5.638530 ATTTACCCAAAACCACCACATTT 57.361 34.783 0.00 0.00 0.00 2.32
2426 5296 6.749036 ATTTACCCAAAACCACCACATTTA 57.251 33.333 0.00 0.00 0.00 1.40
2427 5297 6.555463 TTTACCCAAAACCACCACATTTAA 57.445 33.333 0.00 0.00 0.00 1.52
2428 5298 4.681074 ACCCAAAACCACCACATTTAAG 57.319 40.909 0.00 0.00 0.00 1.85
2429 5299 3.389656 ACCCAAAACCACCACATTTAAGG 59.610 43.478 0.00 0.00 0.00 2.69
2430 5300 3.398406 CCAAAACCACCACATTTAAGGC 58.602 45.455 0.00 0.00 0.00 4.35
2431 5301 3.070878 CCAAAACCACCACATTTAAGGCT 59.929 43.478 0.00 0.00 0.00 4.58
2432 5302 4.282195 CCAAAACCACCACATTTAAGGCTA 59.718 41.667 0.00 0.00 0.00 3.93
2433 5303 5.469479 CAAAACCACCACATTTAAGGCTAG 58.531 41.667 0.00 0.00 0.00 3.42
2434 5304 3.366052 ACCACCACATTTAAGGCTAGG 57.634 47.619 0.00 0.00 0.00 3.02
2435 5305 2.025321 ACCACCACATTTAAGGCTAGGG 60.025 50.000 0.00 0.00 0.00 3.53
2436 5306 2.025321 CCACCACATTTAAGGCTAGGGT 60.025 50.000 0.00 0.00 0.00 4.34
2437 5307 3.201266 CCACCACATTTAAGGCTAGGGTA 59.799 47.826 0.00 0.00 0.00 3.69
2438 5308 4.324719 CCACCACATTTAAGGCTAGGGTAA 60.325 45.833 0.00 0.00 0.00 2.85
2439 5309 4.638865 CACCACATTTAAGGCTAGGGTAAC 59.361 45.833 0.00 0.00 0.00 2.50
2440 5310 4.290196 ACCACATTTAAGGCTAGGGTAACA 59.710 41.667 0.00 0.00 39.74 2.41
2441 5311 5.222171 ACCACATTTAAGGCTAGGGTAACAA 60.222 40.000 0.00 0.00 39.74 2.83
2442 5312 5.124936 CCACATTTAAGGCTAGGGTAACAAC 59.875 44.000 0.00 0.00 39.74 3.32
2443 5313 5.944007 CACATTTAAGGCTAGGGTAACAACT 59.056 40.000 0.00 0.00 39.74 3.16
2444 5314 6.433093 CACATTTAAGGCTAGGGTAACAACTT 59.567 38.462 0.00 0.00 39.74 2.66
2445 5315 6.433093 ACATTTAAGGCTAGGGTAACAACTTG 59.567 38.462 0.00 0.00 39.74 3.16
2446 5316 5.829062 TTAAGGCTAGGGTAACAACTTGA 57.171 39.130 0.00 0.00 39.74 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.190122 TGCCTTTCTAACAAGTATAATTGCATG 58.810 33.333 12.62 3.59 33.28 4.06
84 85 4.398988 TGACCAGTACAATTGCATGGATTC 59.601 41.667 23.65 15.09 34.99 2.52
88 89 3.346315 TCTGACCAGTACAATTGCATGG 58.654 45.455 17.98 17.98 37.07 3.66
158 159 2.339403 ACATGCGATGTGTTTGGCA 58.661 47.368 0.00 0.00 43.01 4.92
232 243 5.013495 AGAGAAGAAGACCAAACATGGATCA 59.987 40.000 1.10 0.00 0.00 2.92
233 244 5.353678 CAGAGAAGAAGACCAAACATGGATC 59.646 44.000 1.10 0.00 0.00 3.36
234 245 5.013495 TCAGAGAAGAAGACCAAACATGGAT 59.987 40.000 1.10 0.00 0.00 3.41
235 246 4.347876 TCAGAGAAGAAGACCAAACATGGA 59.652 41.667 1.10 0.00 0.00 3.41
237 248 5.303971 AGTCAGAGAAGAAGACCAAACATG 58.696 41.667 0.00 0.00 32.82 3.21
238 249 5.559148 AGTCAGAGAAGAAGACCAAACAT 57.441 39.130 0.00 0.00 32.82 2.71
395 427 0.249280 CGGCTGTGTCTGTGTGTGTA 60.249 55.000 0.00 0.00 0.00 2.90
506 547 0.250166 GGTGGCAGTCCTTGTACGTT 60.250 55.000 0.00 0.00 0.00 3.99
724 765 1.229209 GTGAGGTCCTCCAGGTGGA 60.229 63.158 16.60 6.11 43.08 4.02
905 946 4.235762 GGGATGGCGCCGCTTAGA 62.236 66.667 23.90 2.33 0.00 2.10
952 993 3.512516 GGCTGAGGTTGATGCCGC 61.513 66.667 0.00 0.00 35.79 6.53
1195 1239 3.702045 CCTGAGAGGTCGAAATAGAAGGT 59.298 47.826 0.00 0.00 0.00 3.50
1201 1245 1.134367 CACGCCTGAGAGGTCGAAATA 59.866 52.381 11.66 0.00 37.80 1.40
1513 4373 3.817647 CTGCATAACTCTTATTCCAGGGC 59.182 47.826 0.00 0.00 0.00 5.19
1534 4394 7.831193 ACACATAGCCATCTTGACTTTATTTCT 59.169 33.333 0.00 0.00 0.00 2.52
1596 4458 5.178623 TCATGATGTCGGACAGTTAAAACAC 59.821 40.000 16.84 0.90 0.00 3.32
1688 4558 9.070179 TCGGTCAACTTACATATAGCTATTGTA 57.930 33.333 12.39 15.77 0.00 2.41
1725 4595 5.128827 TCCTCGCATAAAACTGACTTATCCT 59.871 40.000 0.00 0.00 0.00 3.24
1805 4675 7.280356 TCTGGGCCTTTAGATTAAGATACAAC 58.720 38.462 4.53 0.00 0.00 3.32
1806 4676 7.446106 TCTGGGCCTTTAGATTAAGATACAA 57.554 36.000 4.53 0.00 0.00 2.41
1807 4677 7.446106 TTCTGGGCCTTTAGATTAAGATACA 57.554 36.000 4.53 0.00 0.00 2.29
1808 4678 8.622157 GTTTTCTGGGCCTTTAGATTAAGATAC 58.378 37.037 4.53 0.00 0.00 2.24
1809 4679 7.778382 GGTTTTCTGGGCCTTTAGATTAAGATA 59.222 37.037 4.53 0.00 0.00 1.98
1810 4680 6.607600 GGTTTTCTGGGCCTTTAGATTAAGAT 59.392 38.462 4.53 0.00 0.00 2.40
1811 4681 5.949952 GGTTTTCTGGGCCTTTAGATTAAGA 59.050 40.000 4.53 0.00 0.00 2.10
1841 4711 6.687604 AGTCGTCTGAAAATTAATTTTGGGG 58.312 36.000 26.69 16.66 39.86 4.96
1888 4758 7.728981 AGGTGAAATCTATACTATTTCCTCGGA 59.271 37.037 10.95 0.00 40.89 4.55
1936 4806 9.534565 TCGGAGAAGTATAGAAGAATTGAAATG 57.465 33.333 0.00 0.00 0.00 2.32
1957 4827 6.210287 AGTTGAAGGTCTAAAGTATCGGAG 57.790 41.667 0.00 0.00 0.00 4.63
1962 4832 5.169295 GTGCGAGTTGAAGGTCTAAAGTAT 58.831 41.667 0.00 0.00 0.00 2.12
2020 4890 3.644966 TCAGAGGGCGATAAAAACCAT 57.355 42.857 0.00 0.00 0.00 3.55
2021 4891 3.054728 TGATCAGAGGGCGATAAAAACCA 60.055 43.478 0.00 0.00 0.00 3.67
2022 4892 3.541632 TGATCAGAGGGCGATAAAAACC 58.458 45.455 0.00 0.00 0.00 3.27
2023 4893 5.560966 TTTGATCAGAGGGCGATAAAAAC 57.439 39.130 0.00 0.00 0.00 2.43
2024 4894 6.458206 CGATTTTGATCAGAGGGCGATAAAAA 60.458 38.462 0.00 0.00 37.52 1.94
2025 4895 5.007626 CGATTTTGATCAGAGGGCGATAAAA 59.992 40.000 0.00 0.00 0.00 1.52
2026 4896 4.511454 CGATTTTGATCAGAGGGCGATAAA 59.489 41.667 0.00 0.00 0.00 1.40
2027 4897 4.058124 CGATTTTGATCAGAGGGCGATAA 58.942 43.478 0.00 0.00 0.00 1.75
2028 4898 3.320826 TCGATTTTGATCAGAGGGCGATA 59.679 43.478 0.00 0.00 0.00 2.92
2029 4899 2.103094 TCGATTTTGATCAGAGGGCGAT 59.897 45.455 0.00 0.00 0.00 4.58
2030 4900 1.480545 TCGATTTTGATCAGAGGGCGA 59.519 47.619 0.00 0.76 0.00 5.54
2031 4901 1.939974 TCGATTTTGATCAGAGGGCG 58.060 50.000 0.00 0.00 0.00 6.13
2032 4902 3.009723 TGTTCGATTTTGATCAGAGGGC 58.990 45.455 0.00 0.00 0.00 5.19
2033 4903 5.824904 AATGTTCGATTTTGATCAGAGGG 57.175 39.130 0.00 0.00 0.00 4.30
2034 4904 8.834465 AGATTAATGTTCGATTTTGATCAGAGG 58.166 33.333 0.00 0.00 0.00 3.69
2039 4909 9.784824 CGACTAGATTAATGTTCGATTTTGATC 57.215 33.333 0.00 0.00 0.00 2.92
2040 4910 9.529325 TCGACTAGATTAATGTTCGATTTTGAT 57.471 29.630 5.54 0.00 0.00 2.57
2041 4911 8.920509 TCGACTAGATTAATGTTCGATTTTGA 57.079 30.769 5.54 0.00 0.00 2.69
2045 4915 9.613957 CACTATCGACTAGATTAATGTTCGATT 57.386 33.333 20.62 7.42 40.66 3.34
2046 4916 9.000486 TCACTATCGACTAGATTAATGTTCGAT 58.000 33.333 19.79 19.79 40.66 3.59
2047 4917 8.281194 GTCACTATCGACTAGATTAATGTTCGA 58.719 37.037 10.65 10.65 40.66 3.71
2048 4918 8.068380 TGTCACTATCGACTAGATTAATGTTCG 58.932 37.037 0.00 0.00 40.66 3.95
2049 4919 9.900710 ATGTCACTATCGACTAGATTAATGTTC 57.099 33.333 0.00 0.00 40.66 3.18
2054 4924 9.774413 TGAGTATGTCACTATCGACTAGATTAA 57.226 33.333 0.00 0.00 40.66 1.40
2055 4925 9.425577 CTGAGTATGTCACTATCGACTAGATTA 57.574 37.037 0.00 0.00 40.66 1.75
2056 4926 8.151596 TCTGAGTATGTCACTATCGACTAGATT 58.848 37.037 0.00 0.00 40.66 2.40
2057 4927 7.601130 GTCTGAGTATGTCACTATCGACTAGAT 59.399 40.741 0.00 0.00 43.19 1.98
2058 4928 6.924612 GTCTGAGTATGTCACTATCGACTAGA 59.075 42.308 0.00 0.00 37.72 2.43
2059 4929 6.146510 GGTCTGAGTATGTCACTATCGACTAG 59.853 46.154 0.00 0.00 37.72 2.57
2060 4930 5.990386 GGTCTGAGTATGTCACTATCGACTA 59.010 44.000 0.00 0.00 37.72 2.59
2061 4931 4.817464 GGTCTGAGTATGTCACTATCGACT 59.183 45.833 0.00 0.00 37.72 4.18
2062 4932 4.023878 GGGTCTGAGTATGTCACTATCGAC 60.024 50.000 0.00 0.00 37.72 4.20
2063 4933 4.135306 GGGTCTGAGTATGTCACTATCGA 58.865 47.826 0.00 0.00 37.72 3.59
2064 4934 4.138290 AGGGTCTGAGTATGTCACTATCG 58.862 47.826 0.00 0.00 37.72 2.92
2065 4935 5.830991 AGAAGGGTCTGAGTATGTCACTATC 59.169 44.000 0.00 0.00 37.72 2.08
2066 4936 5.772004 AGAAGGGTCTGAGTATGTCACTAT 58.228 41.667 0.00 0.00 37.72 2.12
2067 4937 5.194473 AGAAGGGTCTGAGTATGTCACTA 57.806 43.478 0.00 0.00 37.72 2.74
2068 4938 4.054359 AGAAGGGTCTGAGTATGTCACT 57.946 45.455 0.00 0.00 41.47 3.41
2069 4939 4.810191 AAGAAGGGTCTGAGTATGTCAC 57.190 45.455 0.00 0.00 33.05 3.67
2070 4940 4.223032 GGAAAGAAGGGTCTGAGTATGTCA 59.777 45.833 0.00 0.00 33.05 3.58
2071 4941 4.223032 TGGAAAGAAGGGTCTGAGTATGTC 59.777 45.833 0.00 0.00 33.05 3.06
2072 4942 4.168101 TGGAAAGAAGGGTCTGAGTATGT 58.832 43.478 0.00 0.00 33.05 2.29
2073 4943 4.826274 TGGAAAGAAGGGTCTGAGTATG 57.174 45.455 0.00 0.00 33.05 2.39
2074 4944 5.843019 TTTGGAAAGAAGGGTCTGAGTAT 57.157 39.130 0.00 0.00 33.05 2.12
2075 4945 5.309543 TCATTTGGAAAGAAGGGTCTGAGTA 59.690 40.000 0.00 0.00 33.05 2.59
2076 4946 4.104738 TCATTTGGAAAGAAGGGTCTGAGT 59.895 41.667 0.00 0.00 33.05 3.41
2077 4947 4.655963 TCATTTGGAAAGAAGGGTCTGAG 58.344 43.478 0.00 0.00 33.05 3.35
2078 4948 4.350816 TCTCATTTGGAAAGAAGGGTCTGA 59.649 41.667 0.00 0.00 33.05 3.27
2079 4949 4.655963 TCTCATTTGGAAAGAAGGGTCTG 58.344 43.478 0.00 0.00 33.05 3.51
2080 4950 5.073428 GTTCTCATTTGGAAAGAAGGGTCT 58.927 41.667 0.00 0.00 34.72 3.85
2081 4951 4.218635 GGTTCTCATTTGGAAAGAAGGGTC 59.781 45.833 0.00 0.00 30.07 4.46
2082 4952 4.152647 GGTTCTCATTTGGAAAGAAGGGT 58.847 43.478 0.00 0.00 30.07 4.34
2083 4953 4.151883 TGGTTCTCATTTGGAAAGAAGGG 58.848 43.478 0.00 0.00 30.07 3.95
2084 4954 5.990120 ATGGTTCTCATTTGGAAAGAAGG 57.010 39.130 0.00 0.00 30.55 3.46
2085 4955 8.964772 AGAATATGGTTCTCATTTGGAAAGAAG 58.035 33.333 0.00 0.00 37.30 2.85
2086 4956 8.884124 AGAATATGGTTCTCATTTGGAAAGAA 57.116 30.769 0.00 0.00 37.30 2.52
2087 4957 8.884124 AAGAATATGGTTCTCATTTGGAAAGA 57.116 30.769 0.00 0.00 37.30 2.52
2088 4958 9.933723 AAAAGAATATGGTTCTCATTTGGAAAG 57.066 29.630 0.00 0.00 37.30 2.62
2113 4983 4.473477 TTCCTTTCTTTTGCGGGAAAAA 57.527 36.364 8.74 0.00 33.04 1.94
2114 4984 4.473477 TTTCCTTTCTTTTGCGGGAAAA 57.527 36.364 7.21 7.21 41.29 2.29
2115 4985 4.185394 GTTTTCCTTTCTTTTGCGGGAAA 58.815 39.130 0.00 0.00 42.13 3.13
2116 4986 3.431068 GGTTTTCCTTTCTTTTGCGGGAA 60.431 43.478 0.00 0.00 36.94 3.97
2117 4987 2.101750 GGTTTTCCTTTCTTTTGCGGGA 59.898 45.455 0.00 0.00 36.94 5.14
2118 4988 2.159028 TGGTTTTCCTTTCTTTTGCGGG 60.159 45.455 0.00 0.00 41.38 6.13
2119 4989 3.172229 TGGTTTTCCTTTCTTTTGCGG 57.828 42.857 0.00 0.00 41.38 5.69
2120 4990 5.733226 AAATGGTTTTCCTTTCTTTTGCG 57.267 34.783 0.00 0.00 41.38 4.85
2121 4991 7.908082 GTGTAAAATGGTTTTCCTTTCTTTTGC 59.092 33.333 0.00 0.00 41.38 3.68
2122 4992 8.940952 TGTGTAAAATGGTTTTCCTTTCTTTTG 58.059 29.630 0.00 0.00 41.38 2.44
2123 4993 9.161629 CTGTGTAAAATGGTTTTCCTTTCTTTT 57.838 29.630 0.00 0.00 41.38 2.27
2124 4994 8.536175 TCTGTGTAAAATGGTTTTCCTTTCTTT 58.464 29.630 0.00 0.00 41.38 2.52
2125 4995 8.073467 TCTGTGTAAAATGGTTTTCCTTTCTT 57.927 30.769 0.00 0.00 41.38 2.52
2126 4996 7.654022 TCTGTGTAAAATGGTTTTCCTTTCT 57.346 32.000 0.00 0.00 41.38 2.52
2127 4997 7.979537 ACTTCTGTGTAAAATGGTTTTCCTTTC 59.020 33.333 0.00 0.00 41.38 2.62
2128 4998 7.763985 CACTTCTGTGTAAAATGGTTTTCCTTT 59.236 33.333 0.00 0.00 38.87 3.11
2129 4999 7.264947 CACTTCTGTGTAAAATGGTTTTCCTT 58.735 34.615 0.00 0.00 38.87 3.36
2130 5000 6.682861 GCACTTCTGTGTAAAATGGTTTTCCT 60.683 38.462 0.00 0.00 45.44 3.36
2131 5001 5.462068 GCACTTCTGTGTAAAATGGTTTTCC 59.538 40.000 0.00 0.00 45.44 3.13
2132 5002 5.462068 GGCACTTCTGTGTAAAATGGTTTTC 59.538 40.000 0.00 0.00 45.44 2.29
2133 5003 5.105146 TGGCACTTCTGTGTAAAATGGTTTT 60.105 36.000 0.00 0.00 45.44 2.43
2134 5004 4.404073 TGGCACTTCTGTGTAAAATGGTTT 59.596 37.500 0.00 0.00 45.44 3.27
2135 5005 3.957497 TGGCACTTCTGTGTAAAATGGTT 59.043 39.130 0.00 0.00 45.44 3.67
2185 5055 7.239763 TCACCTTGTTTGTAGTCTCATGATA 57.760 36.000 0.00 0.00 0.00 2.15
2202 5072 8.576442 AGTCATTTTGGTAAACTTATCACCTTG 58.424 33.333 0.00 0.00 33.28 3.61
2246 5116 3.717294 GAGGGAAGGAAGCGGGCA 61.717 66.667 0.00 0.00 0.00 5.36
2253 5123 3.983533 TTTGGGAAAAGAGGGAAGGAA 57.016 42.857 0.00 0.00 0.00 3.36
2282 5152 4.785376 ACCATAGAAAGGACTGATCAAGGT 59.215 41.667 0.00 0.00 0.00 3.50
2313 5183 4.674281 ACAAAGTATTTCCCCGCAAAAA 57.326 36.364 0.00 0.00 35.03 1.94
2314 5184 5.986501 ATACAAAGTATTTCCCCGCAAAA 57.013 34.783 0.00 0.00 35.03 2.44
2315 5185 5.986501 AATACAAAGTATTTCCCCGCAAA 57.013 34.783 0.00 0.00 35.03 3.68
2316 5186 6.181908 AGTAATACAAAGTATTTCCCCGCAA 58.818 36.000 7.61 0.00 35.03 4.85
2317 5187 5.747342 AGTAATACAAAGTATTTCCCCGCA 58.253 37.500 7.61 0.00 35.03 5.69
2318 5188 5.818857 TGAGTAATACAAAGTATTTCCCCGC 59.181 40.000 7.61 0.00 35.03 6.13
2319 5189 7.852971 TTGAGTAATACAAAGTATTTCCCCG 57.147 36.000 7.61 0.00 35.03 5.73
2338 5208 8.812972 TGTTGAGTGTAATCCTACTATTTGAGT 58.187 33.333 0.00 0.00 42.69 3.41
2339 5209 9.823647 ATGTTGAGTGTAATCCTACTATTTGAG 57.176 33.333 0.00 0.00 0.00 3.02
2340 5210 9.599866 CATGTTGAGTGTAATCCTACTATTTGA 57.400 33.333 0.00 0.00 0.00 2.69
2341 5211 9.599866 TCATGTTGAGTGTAATCCTACTATTTG 57.400 33.333 0.00 0.00 0.00 2.32
2342 5212 9.601217 GTCATGTTGAGTGTAATCCTACTATTT 57.399 33.333 0.00 0.00 0.00 1.40
2343 5213 8.758829 TGTCATGTTGAGTGTAATCCTACTATT 58.241 33.333 0.00 0.00 0.00 1.73
2344 5214 8.306313 TGTCATGTTGAGTGTAATCCTACTAT 57.694 34.615 0.00 0.00 0.00 2.12
2345 5215 7.712204 TGTCATGTTGAGTGTAATCCTACTA 57.288 36.000 0.00 0.00 0.00 1.82
2346 5216 6.605471 TGTCATGTTGAGTGTAATCCTACT 57.395 37.500 0.00 0.00 0.00 2.57
2347 5217 7.334421 ACAATGTCATGTTGAGTGTAATCCTAC 59.666 37.037 1.85 0.00 0.00 3.18
2348 5218 7.394016 ACAATGTCATGTTGAGTGTAATCCTA 58.606 34.615 1.85 0.00 0.00 2.94
2349 5219 6.240894 ACAATGTCATGTTGAGTGTAATCCT 58.759 36.000 1.85 0.00 0.00 3.24
2350 5220 6.500684 ACAATGTCATGTTGAGTGTAATCC 57.499 37.500 1.85 0.00 0.00 3.01
2351 5221 6.738200 CGAACAATGTCATGTTGAGTGTAATC 59.262 38.462 1.85 0.00 43.31 1.75
2352 5222 6.426633 TCGAACAATGTCATGTTGAGTGTAAT 59.573 34.615 1.85 0.00 43.31 1.89
2353 5223 5.755861 TCGAACAATGTCATGTTGAGTGTAA 59.244 36.000 1.85 0.00 43.31 2.41
2354 5224 5.176774 GTCGAACAATGTCATGTTGAGTGTA 59.823 40.000 1.85 0.00 43.31 2.90
2355 5225 4.024893 GTCGAACAATGTCATGTTGAGTGT 60.025 41.667 1.85 0.00 43.31 3.55
2356 5226 4.457810 GTCGAACAATGTCATGTTGAGTG 58.542 43.478 1.85 0.00 43.31 3.51
2357 5227 3.184379 CGTCGAACAATGTCATGTTGAGT 59.816 43.478 1.85 0.00 43.31 3.41
2358 5228 3.428534 TCGTCGAACAATGTCATGTTGAG 59.571 43.478 0.00 0.00 43.31 3.02
2359 5229 3.183574 GTCGTCGAACAATGTCATGTTGA 59.816 43.478 0.00 0.00 43.31 3.18
2360 5230 3.469629 GTCGTCGAACAATGTCATGTTG 58.530 45.455 0.00 0.00 43.31 3.33
2361 5231 2.478894 GGTCGTCGAACAATGTCATGTT 59.521 45.455 5.14 0.00 45.82 2.71
2362 5232 2.066262 GGTCGTCGAACAATGTCATGT 58.934 47.619 5.14 0.00 34.24 3.21
2363 5233 2.337583 AGGTCGTCGAACAATGTCATG 58.662 47.619 13.74 0.00 0.00 3.07
2364 5234 2.029380 TGAGGTCGTCGAACAATGTCAT 60.029 45.455 13.74 0.00 0.00 3.06
2365 5235 1.338655 TGAGGTCGTCGAACAATGTCA 59.661 47.619 13.74 4.40 0.00 3.58
2366 5236 2.060326 TGAGGTCGTCGAACAATGTC 57.940 50.000 13.74 1.50 0.00 3.06
2367 5237 2.029380 TGATGAGGTCGTCGAACAATGT 60.029 45.455 13.74 0.00 34.69 2.71
2368 5238 2.600420 CTGATGAGGTCGTCGAACAATG 59.400 50.000 13.74 0.00 34.69 2.82
2369 5239 2.417379 CCTGATGAGGTCGTCGAACAAT 60.417 50.000 13.74 5.60 34.16 2.71
2370 5240 1.067846 CCTGATGAGGTCGTCGAACAA 60.068 52.381 13.74 0.04 34.16 2.83
2371 5241 0.526211 CCTGATGAGGTCGTCGAACA 59.474 55.000 13.74 6.76 34.16 3.18
2372 5242 3.330766 CCTGATGAGGTCGTCGAAC 57.669 57.895 0.80 0.80 34.16 3.95
2386 5256 5.130477 GGGTAAATAACTCATCAGGACCTGA 59.870 44.000 26.28 26.28 44.99 3.86
2387 5257 5.104527 TGGGTAAATAACTCATCAGGACCTG 60.105 44.000 15.99 15.99 31.95 4.00
2388 5258 5.036916 TGGGTAAATAACTCATCAGGACCT 58.963 41.667 0.00 0.00 31.95 3.85
2389 5259 5.367945 TGGGTAAATAACTCATCAGGACC 57.632 43.478 0.00 0.00 31.95 4.46
2390 5260 7.362660 GGTTTTGGGTAAATAACTCATCAGGAC 60.363 40.741 0.00 0.00 38.75 3.85
2391 5261 6.661805 GGTTTTGGGTAAATAACTCATCAGGA 59.338 38.462 0.00 0.00 38.75 3.86
2392 5262 6.435904 TGGTTTTGGGTAAATAACTCATCAGG 59.564 38.462 0.00 0.00 38.75 3.86
2393 5263 7.312899 GTGGTTTTGGGTAAATAACTCATCAG 58.687 38.462 0.00 0.00 38.75 2.90
2394 5264 6.209788 GGTGGTTTTGGGTAAATAACTCATCA 59.790 38.462 0.00 0.00 38.75 3.07
2395 5265 6.209788 TGGTGGTTTTGGGTAAATAACTCATC 59.790 38.462 0.00 0.00 38.75 2.92
2396 5266 6.014925 GTGGTGGTTTTGGGTAAATAACTCAT 60.015 38.462 0.00 0.00 38.75 2.90
2397 5267 5.302313 GTGGTGGTTTTGGGTAAATAACTCA 59.698 40.000 0.00 0.00 36.54 3.41
2398 5268 5.302313 TGTGGTGGTTTTGGGTAAATAACTC 59.698 40.000 0.00 0.00 0.00 3.01
2399 5269 5.209659 TGTGGTGGTTTTGGGTAAATAACT 58.790 37.500 0.00 0.00 0.00 2.24
2400 5270 5.532664 TGTGGTGGTTTTGGGTAAATAAC 57.467 39.130 0.00 0.00 0.00 1.89
2401 5271 6.749036 AATGTGGTGGTTTTGGGTAAATAA 57.251 33.333 0.00 0.00 0.00 1.40
2402 5272 6.749036 AAATGTGGTGGTTTTGGGTAAATA 57.251 33.333 0.00 0.00 0.00 1.40
2403 5273 5.638530 AAATGTGGTGGTTTTGGGTAAAT 57.361 34.783 0.00 0.00 0.00 1.40
2404 5274 6.408206 CCTTAAATGTGGTGGTTTTGGGTAAA 60.408 38.462 0.00 0.00 0.00 2.01
2405 5275 5.070580 CCTTAAATGTGGTGGTTTTGGGTAA 59.929 40.000 0.00 0.00 0.00 2.85
2406 5276 4.589374 CCTTAAATGTGGTGGTTTTGGGTA 59.411 41.667 0.00 0.00 0.00 3.69
2407 5277 3.389656 CCTTAAATGTGGTGGTTTTGGGT 59.610 43.478 0.00 0.00 0.00 4.51
2408 5278 3.805457 GCCTTAAATGTGGTGGTTTTGGG 60.805 47.826 0.00 0.00 0.00 4.12
2409 5279 3.070878 AGCCTTAAATGTGGTGGTTTTGG 59.929 43.478 0.00 0.00 0.00 3.28
2410 5280 4.335400 AGCCTTAAATGTGGTGGTTTTG 57.665 40.909 0.00 0.00 0.00 2.44
2411 5281 4.526650 CCTAGCCTTAAATGTGGTGGTTTT 59.473 41.667 0.00 0.00 0.00 2.43
2412 5282 4.086457 CCTAGCCTTAAATGTGGTGGTTT 58.914 43.478 0.00 0.00 0.00 3.27
2413 5283 3.563479 CCCTAGCCTTAAATGTGGTGGTT 60.563 47.826 0.00 0.00 0.00 3.67
2414 5284 2.025321 CCCTAGCCTTAAATGTGGTGGT 60.025 50.000 0.00 0.00 0.00 4.16
2415 5285 2.025321 ACCCTAGCCTTAAATGTGGTGG 60.025 50.000 0.00 0.00 0.00 4.61
2416 5286 3.366052 ACCCTAGCCTTAAATGTGGTG 57.634 47.619 0.00 0.00 0.00 4.17
2417 5287 4.290196 TGTTACCCTAGCCTTAAATGTGGT 59.710 41.667 0.00 0.00 0.00 4.16
2418 5288 4.850680 TGTTACCCTAGCCTTAAATGTGG 58.149 43.478 0.00 0.00 0.00 4.17
2419 5289 5.944007 AGTTGTTACCCTAGCCTTAAATGTG 59.056 40.000 0.00 0.00 0.00 3.21
2420 5290 6.135819 AGTTGTTACCCTAGCCTTAAATGT 57.864 37.500 0.00 0.00 0.00 2.71
2421 5291 6.657541 TCAAGTTGTTACCCTAGCCTTAAATG 59.342 38.462 2.11 0.00 0.00 2.32
2422 5292 6.786122 TCAAGTTGTTACCCTAGCCTTAAAT 58.214 36.000 2.11 0.00 0.00 1.40
2423 5293 6.190346 TCAAGTTGTTACCCTAGCCTTAAA 57.810 37.500 2.11 0.00 0.00 1.52
2424 5294 5.829062 TCAAGTTGTTACCCTAGCCTTAA 57.171 39.130 2.11 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.