Locus 3172

Sequence ID 2R_DroMel_CAF1
Location 10,833,630 – 10,833,767
Length 137
Max. P 0.967198
window5220 window5221 window5222

overview

Window 0

Location 10,833,630 – 10,833,750
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.78
Mean single sequence MFE -45.77
Consensus MFE -22.40
Energy contribution -23.07
Covariance contribution 0.67
Combinations/Pair 1.17
Mean z-score -2.33
Structure conservation index 0.49
SVM decision value 0.34
SVM RNA-class probability 0.697712
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10833630 120 + 20766785
UGUAGUCCAUGCCUGCCUUCAUGAUCGUGUUUCGGUGCUGUAGCAAAAGUGUUAGACAGAGAAACAUGAGGAAUGCAUUACCUCCACCGAAUUCUGUAGGUGGAGGCAAUGCGGCCGCAG
.........(((..((((((....(((((((((..((.(.(((((....))))).)))..))))))))).))).(((((.((((((((..........)))))))).)))))))).))). ( -47.20)
>DroVir_CAF1 50110 120 + 1
UGUAGUCCAUGGCCGACUUGAUGAUUGUGUUGCGAUGCUGCAGCAACAGGGUCAGGCAGAGAAACAUAAGGAACGCAUUGCCGCCCCCAAAUUCAGCGGGUGGCGGCAGUGCAGCAGCUG
(((..((((((.((..((((((..((((((((((....)))))).)))).))))))..).)...)))..)))..((((((((((((((.........))).))))))))))).))).... ( -49.30)
>DroGri_CAF1 46080 120 + 1
UGUAGUCCAUCGCCGCCUUGAUAAUGGUAUUUCGAUGCUGCAGCAGCAGCGUCAGGCAGAGAAACAUAAGAAAAGCAUUGCCGCCACCAAAUUCACUAGGCGGCGGCAGUGCAGCAGCCG
(((.((...((((((((........))).....((((((((....)))))))).))).))...)).........(((((((((((.((..........)).))))))))))).))).... ( -50.40)
>DroWil_CAF1 63143 120 + 1
UAUAAUCCAUGCCAGCUUUCAUUAUGGUAUUACGAUGUUGCAGGAGUAGAGUCAAACAGAGAAACAUGAGAAAAGCAUUGCCGCCACCAAAUUCACUGGGUGGAGGUAAUGCAGCAGCUG
............((((((((.((((((.....)(((.((((....)))).)))...........))))))))).((((((((.(((((..........))))).))))))))....)))) ( -34.50)
>DroMoj_CAF1 63510 120 + 1
UGUAGUCCAUGCCCGACUUAAUAAUGGUGUUGCGAUGCUGCAGCAGCAGUGUUAGGCAGAGGAACAUAAGGAACGCAUUGCCGCCCCCGAAUUCACCCGGUGGGGGCAGAGCAGCCGCUG
(((..(((.((((..((.......((.(((((((....))))))).))..))..))))..)))..))).((...((.(((((.((((((........))).)))))))).))..)).... ( -46.20)
>DroAna_CAF1 40820 120 + 1
UGUAGUCCAUGGCCCCCUUGAUGAUGGUGUUCCUGUGCUGCAGCAGCAGGGUGAGGCAGAGGAACAUGAGGAAGGCAUUACCGCCACCGAACUCAGACGGCGGAGGCAGAGCCGCCGCCG
((.((((..((((..((((.......((((((((.((((.((.(.....).)).)))).))))))))))))..((.....))))))..).)))))..((((((.(((...))).)))))) ( -47.01)
>consensus
UGUAGUCCAUGCCCGCCUUGAUGAUGGUGUUGCGAUGCUGCAGCAGCAGGGUCAGGCAGAGAAACAUAAGGAAAGCAUUGCCGCCACCAAAUUCACUAGGUGGAGGCAGUGCAGCAGCUG
..........................(((((.(..((((...((......))..))))..).))))).......((((((((.((.((..........)).)).))))))))........ (-22.40 = -23.07 +   0.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,833,670 – 10,833,767
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 76.88
Mean single sequence MFE -36.30
Consensus MFE -17.24
Energy contribution -18.02
Covariance contribution 0.78
Combinations/Pair 1.15
Mean z-score -2.37
Structure conservation index 0.47
SVM decision value 1.12
SVM RNA-class probability 0.918567
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10833670 97 + 20766785
UAGCAAAAGUGUUAGACAGAGAAACAUGAGGAAUGCAUUACCUCCACCGAAUUCUGUAGGUGGAGGCAAUGCGGCCGCAGUGGUAUUCACUGCACUG
(((((....)))))..(((..........((..((((((.((((((((..........)))))))).)))))).))((((((.....)))))).))) ( -37.60)
>DroVir_CAF1 50150 94 + 1
CAGCAACAGGGUCAGGCAGAGAAACAUAAGGAACGCAUUGCCGCCCCCAAAUUCAGCGGGUGGCGGCAGUGCAGCAGCUGUGCUAUUGAUCCCG---
........((((((((((.((...(....)....((((((((((((((.........))).))))))))))).....)).))))..))))))..--- ( -41.00)
>DroGri_CAF1 46120 94 + 1
CAGCAGCAGCGUCAGGCAGAGAAACAUAAGAAAAGCAUUGCCGCCACCAAAUUCACUAGGCGGCGGCAGUGCAGCAGCCGUGCUGUUCAGGCCG---
..((.((((((...(((.......(....)....(((((((((((.((..........)).)))))))))))....))).))))))....))..--- ( -38.20)
>DroEre_CAF1 46667 97 + 1
UAGUAGAAGUGUGAGACAGAGAAACAUGAGGAAUGCAUUACCUCCGCCGAAUUCUGUAGGUGGAGGCAAUGCAGCCGCUGUGGUGUUCAGUCCAGUG
...........((.(((.(((...((((.((..((((((.((((((((..........)))))))).)))))).))..))))...))).)))))... ( -33.20)
>DroMoj_CAF1 63550 94 + 1
CAGCAGCAGUGUUAGGCAGAGGAACAUAAGGAACGCAUUGCCGCCCCCGAAUUCACCCGGUGGGGGCAGAGCAGCCGCUGUGCUAUUCAGCCCA---
..(((((.(((((.........)))))..((...((.(((((.((((((........))).)))))))).))..)))))))(((....)))...--- ( -33.20)
>DroAna_CAF1 40860 94 + 1
CAGCAGCAGGGUGAGGCAGAGGAACAUGAGGAAGGCAUUACCGCCACCGAACUCAGACGGCGGAGGCAGAGCCGCCGCCGUGGCGUUUACUCC---G
........(((((((((.(((........((..(((......))).))...)))..(((((((.(((...))).))))))).)).))))).))---. ( -34.60)
>consensus
CAGCAGCAGUGUCAGGCAGAGAAACAUAAGGAACGCAUUACCGCCACCGAAUUCAGUAGGUGGAGGCAGUGCAGCCGCUGUGCUAUUCAGUCCA___
..................(((...(((..((...(((((.(((((.((..........)).))))).)))))..))...)))...)))......... (-17.24 = -18.02 +   0.78)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,833,670 – 10,833,767
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 76.88
Mean single sequence MFE -34.67
Consensus MFE -20.24
Energy contribution -21.60
Covariance contribution 1.36
Combinations/Pair 1.23
Mean z-score -2.31
Structure conservation index 0.58
SVM decision value 1.61
SVM RNA-class probability 0.967198
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10833670 97 - 20766785
CAGUGCAGUGAAUACCACUGCGGCCGCAUUGCCUCCACCUACAGAAUUCGGUGGAGGUAAUGCAUUCCUCAUGUUUCUCUGUCUAACACUUUUGCUA
....((((((.....))))))(((.((((((((((((((..........))))))))))))))........((((.........)))).....))). ( -38.20)
>DroVir_CAF1 50150 94 - 1
---CGGGAUCAAUAGCACAGCUGCUGCACUGCCGCCACCCGCUGAAUUUGGGGGCGGCAAUGCGUUCCUUAUGUUUCUCUGCCUGACCCUGUUGCUG
---.(((.(((...(((.((..((((((.(((((((.((((.......))))))))))).))))........))..)).))).))))))........ ( -34.60)
>DroGri_CAF1 46120 94 - 1
---CGGCCUGAACAGCACGGCUGCUGCACUGCCGCCGCCUAGUGAAUUUGGUGGCGGCAAUGCUUUUCUUAUGUUUCUCUGCCUGACGCUGCUGCUG
---.........(((((((((....(((.((((((((((..........)))))))))).))).........(((.........))))))).))))) ( -37.60)
>DroEre_CAF1 46667 97 - 1
CACUGGACUGAACACCACAGCGGCUGCAUUGCCUCCACCUACAGAAUUCGGCGGAGGUAAUGCAUUCCUCAUGUUUCUCUGUCUCACACUUCUACUA
....((((.(((....((((.((.((((((((((((.((..........)).))))))))))))..)).).))))))...))))............. ( -29.60)
>DroMoj_CAF1 63550 94 - 1
---UGGGCUGAAUAGCACAGCGGCUGCUCUGCCCCCACCGGGUGAAUUCGGGGGCGGCAAUGCGUUCCUUAUGUUCCUCUGCCUAACACUGCUGCUG
---...(((....))).(((((((.((..(((((((.(((((....)))))))).))))..)).....(((.((......)).)))....))))))) ( -33.40)
>DroAna_CAF1 40860 94 - 1
C---GGAGUAAACGCCACGGCGGCGGCUCUGCCUCCGCCGUCUGAGUUCGGUGGCGGUAAUGCCUUCCUCAUGUUCCUCUGCCUCACCCUGCUGCUG
.---((.(....).)).((((((((((..((((.((((((........)))))).))))..)))........((......))........))))))) ( -34.60)
>consensus
___UGGACUGAACACCACAGCGGCUGCACUGCCUCCACCUACUGAAUUCGGUGGCGGCAAUGCAUUCCUCAUGUUUCUCUGCCUAACACUGCUGCUG
.................(((((((.(((.(((((((.((..........)).))))))).))).........(((.........)))...))))))) (-20.24 = -21.60 +   1.36)

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 10:49:12 2006