Locus 4827

Sequence ID 3R_DroMel_CAF1
Location 12,622,779 – 12,622,869
Length 90
Max. P 0.719272
window7913 window7914

overview

Window 3

Location 12,622,779 – 12,622,869
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.96
Mean single sequence MFE -25.62
Consensus MFE -19.39
Energy contribution -20.28
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -1.33
Structure conservation index 0.76
SVM decision value 0.40
SVM RNA-class probability 0.719272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12622779 90 + 27905053
----------------------------CAGCAGCUCCGAAUGUGGACGAAAACUUUUUAGACUUUUUGUCGACUUUUCGCAUUUUUAGUUGCGGCCAAGUGGAAAGUGCUGCCUCAG--
----------------------------..(((((((((...((.((((((((.((....)).)))))))).))...(((((........))))).....))))....))))).....-- ( -25.00)
>DroPse_CAF1 111760 118 + 1
CUCCUCCUCUUCUUUUCUCCUCUCCUUGAAGCCACCCCGAAAGCGGACGAAAAGUUUUUAGACUUUUUGUCGACUUUUCGCAUUUCUAGUUGCGGCCAAGUUGAAAGUGCUGCCUCAG--
..........................(((.((((((((....).)).(((((((((....)))))))))(((((((.(((((........)))))..)))))))..)))..)).))).-- ( -27.70)
>DroSim_CAF1 105951 92 + 1
----------------------------CAGCAGCUCCGAAUGUGGACGAAAACUUUUUAGACUUUUUGUCGACUUUUCGCAUUUUUAGUUGCGGACAAGUGGAAAGUGCUGCCUCAGCA
----------------------------..(((((((((....)))).....(((((((.(((.....))).((((((((((........)))))).))))))))))))))))....... ( -26.70)
>DroYak_CAF1 105512 90 + 1
----------------------------CAGCAGCUCCGAAUGUGAACGAAAACUUUUUAGACUUUUUGUCGACUUUUCGCAUUUUUAGUUGCGGCCAAGUGGAAAGUGCUGCCUCAG--
----------------------------..((((((..(((((((((.(((.....))).(((.....))).....)))))))))..))))))(((..(((.......))))))....-- ( -22.90)
>DroAna_CAF1 101052 90 + 1
----------------------------CAGCAGCUACGAAUGUGGACGAAAACUUUUUAGACUUUUUGUCGACUUUUCGCAUUUUUAGUUGCGGCCAAGUUGAAAGUGCUGCCUCAG--
----------------------------..(((((((.(((((((((((((((.((....)).)))))))).......))))))).)))))))(((..(((.......))))))....-- ( -25.91)
>DroPer_CAF1 118038 118 + 1
CUCCUCCUCUUCUUUUCUCCUCUCCUUCAAGCCACCCCGAAAGCGGACGAAAAGUUUUUAGACUUUUUGUCGACUUUUCGCAUUUCUAGUUGCGGCCAAGUUGAAAGUGCUGCCUCAG--
.............................((((.((.(....).)).(((((((((....)))))))))(((((((.(((((........)))))..)))))))..).))).......-- ( -25.50)
>consensus
____________________________CAGCAGCUCCGAAUGUGGACGAAAACUUUUUAGACUUUUUGUCGACUUUUCGCAUUUUUAGUUGCGGCCAAGUGGAAAGUGCUGCCUCAG__
..............................((((((..(((((((((((((((.((....)).)))))))).......)))))))..))))))(((..(((.......))))))...... (-19.39 = -20.28 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,622,779 – 12,622,869
Length 90
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.96
Mean single sequence MFE -24.12
Consensus MFE -17.44
Energy contribution -17.50
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -1.06
Structure conservation index 0.72
SVM decision value -0.04
SVM RNA-class probability 0.510880
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12622779 90 - 27905053
--CUGAGGCAGCACUUUCCACUUGGCCGCAACUAAAAAUGCGAAAAGUCGACAAAAAGUCUAAAAAGUUUUCGUCCACAUUCGGAGCUGCUG----------------------------
--....(((((((((((..((((...((((........))))..)))).(((.....)))...))))).....(((......))))))))).---------------------------- ( -22.30)
>DroPse_CAF1 111760 118 - 1
--CUGAGGCAGCACUUUCAACUUGGCCGCAACUAGAAAUGCGAAAAGUCGACAAAAAGUCUAAAAACUUUUCGUCCGCUUUCGGGGUGGCUUCAAGGAGAGGAGAAAAGAAGAGGAGGAG
--...........(((((.....((((((..........(((((((((.(((.....))).....)))))))))(((....))).)))))).....)))))................... ( -28.50)
>DroSim_CAF1 105951 92 - 1
UGCUGAGGCAGCACUUUCCACUUGUCCGCAACUAAAAAUGCGAAAAGUCGACAAAAAGUCUAAAAAGUUUUCGUCCACAUUCGGAGCUGCUG----------------------------
......(((((((((((..((((...((((........))))..)))).(((.....)))...))))).....(((......))))))))).---------------------------- ( -22.30)
>DroYak_CAF1 105512 90 - 1
--CUGAGGCAGCACUUUCCACUUGGCCGCAACUAAAAAUGCGAAAAGUCGACAAAAAGUCUAAAAAGUUUUCGUUCACAUUCGGAGCUGCUG----------------------------
--....(((((((((((..((((...((((........))))..)))).(((.....)))...))))).((((........)))))))))).---------------------------- ( -21.60)
>DroAna_CAF1 101052 90 - 1
--CUGAGGCAGCACUUUCAACUUGGCCGCAACUAAAAAUGCGAAAAGUCGACAAAAAGUCUAAAAAGUUUUCGUCCACAUUCGUAGCUGCUG----------------------------
--....((((((.........((((......))))...((((((..((.(((.((((.(......).)))).))).)).)))))))))))).---------------------------- ( -20.10)
>DroPer_CAF1 118038 118 - 1
--CUGAGGCAGCACUUUCAACUUGGCCGCAACUAGAAAUGCGAAAAGUCGACAAAAAGUCUAAAAACUUUUCGUCCGCUUUCGGGGUGGCUUGAAGGAGAGGAGAAAAGAAGAGGAGGAG
--...........(((((.((((...((((........))))..)))).(((.....)))......((((((.(((.((((((((....))))))))...)))))))))....))))).. ( -29.90)
>consensus
__CUGAGGCAGCACUUUCAACUUGGCCGCAACUAAAAAUGCGAAAAGUCGACAAAAAGUCUAAAAAGUUUUCGUCCACAUUCGGAGCUGCUG____________________________
......((((((((((((.((((...((((........))))..)))).))....))))..........((((........))))))))))............................. (-17.44 = -17.50 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:51 2006