Locus 653

Sequence ID 2L_DroMel_CAF1
Location 1,956,248 – 1,956,355
Length 107
Max. P 0.928392
window1071 window1072

overview

Window 1

Location 1,956,248 – 1,956,355
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.92
Mean single sequence MFE -23.12
Consensus MFE -18.51
Energy contribution -18.39
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.08
Structure conservation index 0.80
SVM decision value 1.19
SVM RNA-class probability 0.928392
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1956248 107 + 22407834
AACAGCGUGAUUAAC------UGGAAGCUAAAUGAACGGCACAUA---CUGAAAUGUGCAAUCUGCAUUUAGUUGAAUAAAUAAACGCAGUGAAAAAAGGCAGCAACGAGGGGAAA----
....((((.......------....(((((((((....((((((.---.....))))))......)))))))))..........))))............................---- ( -23.10)
>DroSim_CAF1 599 107 + 1
AACAGCGUGAUUAAC------UGGAAGCUAAAUGAACGGCACAUA---CUGAAAUGUGCAAUCUGCAUUUAGUUGAAUAAAUAAACGCAGUGAAAAAAGGCAGCAACGAGGGGAAA----
....((((.......------....(((((((((....((((((.---.....))))))......)))))))))..........))))............................---- ( -23.10)
>DroEre_CAF1 7890 111 + 1
AACAGCGUGAUUAAC------UGGAAGCUAAAUGAACGGCACAUG---CUGAAAUGUGCAAUCUGCAUUUAGUUGAAUAAAUAAACGCAGUGAAAAAAGGCAGCAACGAGGGGAAAAUGG
.....(((..((..(------(.(.(((((((((....((((((.---.....))))))......)))))))))............((..(....)...)).....).))..))..))). ( -24.40)
>DroYak_CAF1 5597 113 + 1
AACAGCGUGAUUAACUACUACUGAAAGCUAAAUGAACGGCACAUG---CUGAAAUGUGCAAUCUGCAUUUAGUUGAAUAAAUAAACGCGGUGAAAAAAGGCAGCGACGAGGGGAAA----
..(..(((.................(((((((((....((((((.---.....))))))......)))))))))...........(((.((........)).))))))..).....---- ( -24.90)
>DroAna_CAF1 28331 98 + 1
AACAGCGUUAUUAAC------UGGAAACGAAAUGACCUGCACAUGAUGCAGAAAUGUGCAAUCUGCAUUUAGUUGAAUAAAUAAAUGCAACAAAAAAA-----CAACGA-----------
...((.((((((...------((....)).))))))))((((((.........))))))....((((((((..........)))))))).........-----......----------- ( -20.10)
>consensus
AACAGCGUGAUUAAC______UGGAAGCUAAAUGAACGGCACAUG___CUGAAAUGUGCAAUCUGCAUUUAGUUGAAUAAAUAAACGCAGUGAAAAAAGGCAGCAACGAGGGGAAA____
....((((.................(((((((((....((((((.........))))))......)))))))))..........))))................................ (-18.51 = -18.39 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,956,248 – 1,956,355
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.92
Mean single sequence MFE -20.52
Consensus MFE -14.90
Energy contribution -15.22
Covariance contribution 0.32
Combinations/Pair 1.14
Mean z-score -1.85
Structure conservation index 0.73
SVM decision value 0.37
SVM RNA-class probability 0.708712
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1956248 107 - 22407834
----UUUCCCCUCGUUGCUGCCUUUUUUCACUGCGUUUAUUUAUUCAACUAAAUGCAGAUUGCACAUUUCAG---UAUGUGCCGUUCAUUUAGCUUCCA------GUUAAUCACGCUGUU
----............((((..........(((((((((.((....)).)))))))))...((((((.....---.))))))........))))...((------((.......)))).. ( -21.20)
>DroSim_CAF1 599 107 - 1
----UUUCCCCUCGUUGCUGCCUUUUUUCACUGCGUUUAUUUAUUCAACUAAAUGCAGAUUGCACAUUUCAG---UAUGUGCCGUUCAUUUAGCUUCCA------GUUAAUCACGCUGUU
----............((((..........(((((((((.((....)).)))))))))...((((((.....---.))))))........))))...((------((.......)))).. ( -21.20)
>DroEre_CAF1 7890 111 - 1
CCAUUUUCCCCUCGUUGCUGCCUUUUUUCACUGCGUUUAUUUAUUCAACUAAAUGCAGAUUGCACAUUUCAG---CAUGUGCCGUUCAUUUAGCUUCCA------GUUAAUCACGCUGUU
................((((..........(((((((((.((....)).)))))))))...((((((.....---.))))))........))))...((------((.......)))).. ( -20.50)
>DroYak_CAF1 5597 113 - 1
----UUUCCCCUCGUCGCUGCCUUUUUUCACCGCGUUUAUUUAUUCAACUAAAUGCAGAUUGCACAUUUCAG---CAUGUGCCGUUCAUUUAGCUUUCAGUAGUAGUUAAUCACGCUGUU
----............((((............(((((((.((....)).))))))).((..((((((.....---.))))))...))...))))...((((.((........)))))).. ( -18.30)
>DroAna_CAF1 28331 98 - 1
-----------UCGUUG-----UUUUUUUGUUGCAUUUAUUUAUUCAACUAAAUGCAGAUUGCACAUUUCUGCAUCAUGUGCAGGUCAUUUCGUUUCCA------GUUAAUAACGCUGUU
-----------.(((((-----((...(((.((((((((.((....)).))))))))((((((((((.........))))))).)))..........))------)..)))))))..... ( -21.40)
>consensus
____UUUCCCCUCGUUGCUGCCUUUUUUCACUGCGUUUAUUUAUUCAACUAAAUGCAGAUUGCACAUUUCAG___CAUGUGCCGUUCAUUUAGCUUCCA______GUUAAUCACGCUGUU
................((((..........(((((((((.((....)).)))))))))...((((((.........))))))........)))).......................... (-14.90 = -15.22 +   0.32)

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 09:42:05 2006