Locus 3510

Sequence ID 3L_DroMel_CAF1
Location 10,292,942 – 10,293,051
Length 109
Max. P 0.991889
window5480 window5481 window5482

overview

Window 0

Location 10,292,942 – 10,293,034
Length 92
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 79.12
Mean single sequence MFE -19.17
Consensus MFE -15.19
Energy contribution -15.22
Covariance contribution 0.03
Combinations/Pair 1.10
Mean z-score -2.02
Structure conservation index 0.79
SVM decision value 1.31
SVM RNA-class probability 0.940157
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10292942 92 + 23771897
CGUUUACAACAUGACUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUUGUU
.....(((((((((.((......)).)))...((((((...((((((((((.((....))....))))))))))..))))))...)))))). ( -22.30)
>DroVir_CAF1 201079 83 + 1
-----ACAAAGUAA----CUUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUGAAAUGAUAAUUUGUGUGCAGCCAAGUGUUUUUGUAGCU
-----((((((..(----((((((....(((((....)))))(((((((((.............))))))))))))))))..)))))).... ( -22.32)
>DroPse_CAF1 180810 76 + 1
---------CA---CAGCAACGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGGUUUUUU----
---------((---(.......(((......))).......((((((((((.((....))....))))))))))....))).......---- ( -14.50)
>DroGri_CAF1 181297 83 + 1
-----CCAAAGUAA----CUUGACAAUCAAAUGCAUUUAUUUUGCAUAUAAUUGAAAUGAUAAUUUGUGUGCAACAAAGUGUUUUUGUAUAU
-----.........----.........((((.((((((...((((((((((.............))))))))))..)))))).))))..... ( -15.22)
>DroEre_CAF1 178466 92 + 1
CGUUUACAACAUGGCUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUAGUU
...((((((....(((.....)))........((((((...((((((((((.((....))....))))))))))..))))))..)))))).. ( -21.10)
>DroAna_CAF1 179155 80 + 1
------------GGUUGGCUUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUGGUU
------------.........(((...((((.((((((...((((((((((.((....))....))))))))))..)))))).))))..))) ( -19.60)
>consensus
_____ACAACAUGACUGGCUUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUAGUU
...........................((((.((((((...((((((((((.............))))))))))..)))))).))))..... (-15.19 = -15.22 +   0.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,292,942 – 10,293,034
Length 92
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 79.12
Mean single sequence MFE -14.48
Consensus MFE -6.95
Energy contribution -7.15
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.48
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10292942 92 - 23771897
AACAACAAAAGCACUUGACUGCACACAAAUUAUCAUUUGAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGCCAGCCCAGUCAUGUUGUAAACG
.((((((........((((((..(.(((((....)))))(((((.(((((.......))))).)))))....)..))))))))))))..... ( -19.10)
>DroVir_CAF1 201079 83 - 1
AGCUACAAAAACACUUGGCUGCACACAAAUUAUCAUUUCAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGCCAAG----UUACUUUGU-----
....(((((...(((((((((....))............(((((.(((((.......))))).)))))))))))----)...)))))----- ( -17.40)
>DroPse_CAF1 180810 76 - 1
----AAAAAACCACUUGACUGCACACAAAUUAUCAUUUGAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGCCGUUGCUG---UG---------
----.......(((..(((.((...(((((....)))))(((((.(((((.......))))).))))))).)))...)---))--------- ( -13.50)
>DroGri_CAF1 181297 83 - 1
AUAUACAAAAACACUUUGUUGCACACAAAUUAUCAUUUCAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGUCAAG----UUACUUUGG-----
....(((((.....)))))......((((.((......((((((.(((((.......))))).)))))).....----.)).)))).----- ( -12.10)
>DroEre_CAF1 178466 92 - 1
AACUACAAAAGCACUUGACUGCACACAAAUUAUCAUUUGAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGCCAGCCCAGCCAUGUUGUAAACG
...(((((.....((.(.((((...(((((....)))))(((((.(((((.......))))).)))))).))).).)).....))))).... ( -13.90)
>DroAna_CAF1 179155 80 - 1
AACCACAAAAGCACUUGACUGCACACAAAUUAUCAUUUGAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGCCAAGCCAACC------------
.............((((...((...(((((....)))))(((((.(((((.......))))).)))))))))))......------------ ( -10.90)
>consensus
AACUACAAAAGCACUUGACUGCACACAAAUUAUCAUUUGAAUUAUAUGCAAAAUAAAUGCAUUUGAUUGCCAAGCCAGUCAUGUUGU_____
....................((...(((((....)))))(((((.(((((.......))))).)))))))...................... ( -6.95 =  -7.15 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,292,955 – 10,293,051
Length 96
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 86.58
Mean single sequence MFE -31.63
Consensus MFE -26.04
Energy contribution -28.52
Covariance contribution 2.47
Combinations/Pair 1.06
Mean z-score -4.65
Structure conservation index 0.82
SVM decision value 2.29
SVM RNA-class probability 0.991889
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10292955 96 + 23771897
ACUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUUGUUGCCAGCUUGCAGUUGUG
((((((((((((((((((.((((((...((((((((((.((....))....))))))))))..)))))).))))..))))))))))..)))).... ( -37.60)
>DroPse_CAF1 180812 74 + 1
-CAGCAACGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGGUUUUUU---------------------
-..((....)).........(((((...((((((((((.((....))....))))))))))..))))).......--------------------- ( -13.80)
>DroSim_CAF1 174422 96 + 1
GCUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUAGUUGCCAGCUUGCAGUUGUG
((.(((((((((((((((.((((((...((((((((((.((....))....))))))))))..)))))).))))..)))))))))))))....... ( -38.10)
>DroEre_CAF1 178479 96 + 1
GCUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUAGUUGCCAGUUUGCAGUUGUG
((.(((((((((((((((.((((((...((((((((((.((....))....))))))))))..)))))).))))..)))))))))))))....... ( -35.60)
>DroYak_CAF1 176554 96 + 1
GCUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUAGUUGCCAGCUUGCAGUUGUG
((.(((((((((((((((.((((((...((((((((((.((....))....))))))))))..)))))).))))..)))))))))))))....... ( -38.10)
>DroAna_CAF1 179156 94 + 1
GUUGGCUUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUGGUUGUC--UUUGUAGUUGUA
....((..((((((((...((((((...((((((((((.((....))....))))))))))..)))))).....))))))))--...))....... ( -26.60)
>consensus
GCUGGGCUGGCAAUCAAAUGCAUUUAUUUUGCAUAUAAUUCAAAUGAUAAUUUGUGUGCAGUCAAGUGCUUUUGUAGUUGCCAGCUUGCAGUUGUG
...(((((((((((((((.((((((...((((((((((.((....))....))))))))))..)))))).))))..)))))))))))......... (-26.04 = -28.52 +   2.47)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:54 2006