Locus 6123

Sequence ID 2L_DroMel_CAF1
Location 17,122,937 – 17,123,177
Length 240
Max. P 0.999920
window9766 window9767 window9768

overview

Window 6

Location 17,122,937 – 17,123,057
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.17
Mean single sequence MFE -42.88
Consensus MFE -39.00
Energy contribution -39.44
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.30
Structure conservation index 0.91
SVM decision value 3.31
SVM RNA-class probability 0.998971
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17122937 120 + 22407834
UUCCCUCCGGGCGACCACCAUCAGCUAAGUAGAUUUGGGCUACCUGCAUGCAGCUAUGCUGCAGCGUUUAAGUGGGUAUAUAGUAUAUUCCUUUUUUUCCUUCGUGGUGCGGGAGGGAAA
((((((((((....)).(((....((....))...)))((.(((.((.((((((...))))))))....(((.(((((((...))))))))))............))))).)))))))). ( -40.40)
>DroSec_CAF1 86757 118 + 1
UUCCCUCCGGGCGACCACCAUCAGCUAAGUAGAUUUGGGCUACCUGCAUGCAGCUAUGCUGCAGCGUUUAAGUGGGUAUAUAGUAUUUUCC-UUUUUUCCUUGGUGGUGCGGGAG-GAAA
((((..(((.((.(((((((....((....))...)))..((((..(.((((((...))))))........)..)))).............-.........)))).)).)))..)-))). ( -38.20)
>DroSim_CAF1 102820 120 + 1
UUCCCUCCGGGCGACCACCAUCAGCUAAGUAGAUUUGGGCUACCUGCAUGCAGCUAUGCUGCAGCGUUUAAGUGGGUAUAUAGUAUAUUCCGUUUUUUCCUAGGUGGUGUGGGAGGGAAA
((((((((((....)).((((((.(((.(.(((..((((((((.(((.((((((...))))))))).....))))(((((...)))))))))..))).).))).))))).))))))))). ( -43.90)
>DroEre_CAF1 88865 120 + 1
UUCCCUCCGGGCGACCACCAUCAGCUAAGUAGAUUUGGGCUACCUGCAUGCAGCUAUGCUGCAGCGUUUAAGUGGGUAUAUAGUAUAUUCCUUUUUUUGCUCGGCGGUGCGGGAGGGAAA
((((((((((....)).(((((.((..((((((...(((((((.(((.((((((...))))))))).....))))(((((...))))).)))...))))))..)))))).))))))))). ( -46.40)
>DroYak_CAF1 88649 120 + 1
UUCCCUCCGGGCGACCACCAUCAGCUAAGUAGAUUUGGGCUACCUGCAUGCAGCUAUGCUGCAGCGUUUAAGUGGGUAUAUAGUAUAUUUCUUUUUUUACUCGGUGGUGCGGGAGGGAAA
((((((((..((.((((((.............((((((((...(((((.(((....)))))))).))))))))(((((...((.......)).....))))))))))))).)))))))). ( -45.50)
>consensus
UUCCCUCCGGGCGACCACCAUCAGCUAAGUAGAUUUGGGCUACCUGCAUGCAGCUAUGCUGCAGCGUUUAAGUGGGUAUAUAGUAUAUUCCUUUUUUUCCUCGGUGGUGCGGGAGGGAAA
((((((((..((.((((((...((((.((.....)).))))(((..(.((((((...))))))........)..))).........................)))))))).)))))))). (-39.00 = -39.44 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,122,937 – 17,123,057
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.17
Mean single sequence MFE -40.66
Consensus MFE -37.14
Energy contribution -37.62
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -3.61
Structure conservation index 0.91
SVM decision value 4.56
SVM RNA-class probability 0.999920
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17122937 120 - 22407834
UUUCCCUCCCGCACCACGAAGGAAAAAAAGGAAUAUACUAUAUACCCACUUAAACGCUGCAGCAUAGCUGCAUGCAGGUAGCCCAAAUCUACUUAGCUGAUGGUGGUCGCCCGGAGGGAA
.((((((((.(((((((.(.((.......((.((((...)))).)).........((((((((...)))))).))((((((.......))))))..))..).))))).))..)))))))) ( -38.30)
>DroSec_CAF1 86757 118 - 1
UUUC-CUCCCGCACCACCAAGGAAAAAA-GGAAAAUACUAUAUACCCACUUAAACGCUGCAGCAUAGCUGCAUGCAGGUAGCCCAAAUCUACUUAGCUGAUGGUGGUCGCCCGGAGGGAA
.(((-((((.(((((((((.((......-..........................((((((((...)))))).))((((((.......))))))..))..))))))).))..))))))). ( -39.60)
>DroSim_CAF1 102820 120 - 1
UUUCCCUCCCACACCACCUAGGAAAAAACGGAAUAUACUAUAUACCCACUUAAACGCUGCAGCAUAGCUGCAUGCAGGUAGCCCAAAUCUACUUAGCUGAUGGUGGUCGCCCGGAGGGAA
.((((((((..(((((((..((.......((.((((...)))).)).........((((((((...)))))).))((((((.......))))))..))...)))))).)...)))))))) ( -38.80)
>DroEre_CAF1 88865 120 - 1
UUUCCCUCCCGCACCGCCGAGCAAAAAAAGGAAUAUACUAUAUACCCACUUAAACGCUGCAGCAUAGCUGCAUGCAGGUAGCCCAAAUCUACUUAGCUGAUGGUGGUCGCCCGGAGGGAA
.((((((((.((((((((((((.......((.((((...)))).)).........((((((((...)))))).))((((((.......)))))).)))..))))))).))..)))))))) ( -44.30)
>DroYak_CAF1 88649 120 - 1
UUUCCCUCCCGCACCACCGAGUAAAAAAAGAAAUAUACUAUAUACCCACUUAAACGCUGCAGCAUAGCUGCAUGCAGGUAGCCCAAAUCUACUUAGCUGAUGGUGGUCGCCCGGAGGGAA
.((((((((.((((((((((((.................................((((((((...)))))).))((((((.......)))))).)))..))))))).))..)))))))) ( -42.30)
>consensus
UUUCCCUCCCGCACCACCAAGGAAAAAAAGGAAUAUACUAUAUACCCACUUAAACGCUGCAGCAUAGCUGCAUGCAGGUAGCCCAAAUCUACUUAGCUGAUGGUGGUCGCCCGGAGGGAA
.((((((((.(((((((((....................................((((((((...)))))).))((((((.......))))))......))))))).))..)))))))) (-37.14 = -37.62 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,123,057 – 17,123,177
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.75
Mean single sequence MFE -28.30
Consensus MFE -22.00
Energy contribution -24.16
Covariance contribution 2.16
Combinations/Pair 1.09
Mean z-score -1.74
Structure conservation index 0.78
SVM decision value 0.49
SVM RNA-class probability 0.755488
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17123057 120 - 22407834
UCUGGCAAUCGCAAAUCUAGCUGCCUCUCUUUUUCGCUGGAAUUCAUUACAUCAAAUAUAAAGAAAGUUUUAGGCAAUUUGCCAGAAGUCCUGGGAAAAGAGAAGAGCACCGAAAACCCA
(((((((...((.......))))))((((((((((.(.(((.(((.............(((((....)))))(((.....))).))).))).)))))))))))))).............. ( -28.40)
>DroSec_CAF1 86875 120 - 1
UCUGGCAAUCGCAAAUCUAGUUCCCUCUCUUUUUCGCAGGAAUUCAUUACAUCAAAUAUAAAGAAAGUUUUAGGCAAUUUGCCAGAAGUCCUGGGAAAAGAGAAGAGCAGCUAAAACCCA
....((....)).......((((..((((((((((.(((((.(((.............(((((....)))))(((.....))).))).))))))))))))))).))))............ ( -32.50)
>DroSim_CAF1 102940 120 - 1
UCUGGCAAUCGCAAAUCUAGUUGCCUCUCUUUUGCGCUGGAAUUCAUUACAUCAAAUAUAAAGAAAGUUUUAGGCAAUUUGCCAGAAGUCCUGGGAAAAGAGAAGAGCAGCUAAAACCCA
....((....)).....((((((((((((((((.(.(.(((.(((.............(((((....)))))(((.....))).))).))).)).))))))).)).)))))))....... ( -31.40)
>DroEre_CAF1 88985 120 - 1
CCUGGCAAUCGCAAAUCUAGCUGCGUCUCUUUCCCGCUGAAAUUCAUUACAUCAAAUAUAAAGAAAGUUUUAGGCAAUUUGCCAGAAGUCCCGGGAAAAGAGAAAAGCGACCAAAGCCCA
...(((....((.......))(((.(((((((((((..((..(((.............(((((....)))))(((.....))).))).)).)))).)))))))...)))......))).. ( -29.10)
>DroYak_CAF1 88769 120 - 1
CCUGGCAAUCGCAAAUCUAGUUUCGUCUCUCUCUCGCUGAAAUUCAUUACAUCAAAUAUAAAGAAAGUUUUAGGCUAUUUGCCAGAAGUCCCGGGAAAAGAGAAAACCGACUAAAGCCCA
...(((....(.....)(((((...(((((.(((((..((..(((.............(((((....)))))(((.....))).))).)).)))))..))))).....)))))..))).. ( -20.10)
>consensus
UCUGGCAAUCGCAAAUCUAGUUGCCUCUCUUUUUCGCUGGAAUUCAUUACAUCAAAUAUAAAGAAAGUUUUAGGCAAUUUGCCAGAAGUCCUGGGAAAAGAGAAGAGCAACUAAAACCCA
....((....)).....(((((((.((((((((((.(.(((.(((.............(((((....)))))(((.....))).))).))).)))))))))))...)))))))....... (-22.00 = -24.16 +   2.16)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:45 2006