Locus 1590

Sequence ID 2R_DroMel_CAF1
Location 5,959,300 – 5,959,450
Length 150
Max. P 0.991771
window2669 window2670 window2671

overview

Window 9

Location 5,959,300 – 5,959,420
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.17
Mean single sequence MFE -31.26
Consensus MFE -22.82
Energy contribution -22.66
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -2.13
Structure conservation index 0.73
SVM decision value 0.14
SVM RNA-class probability 0.602955
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5959300 120 + 20766785
UAGUGGGAAACGAAAAUGGGCAAAUGAAAUUAGCAUUUAUCAAAUUAUUCCAUUUUCCCAAGGACAGCUUGGCUAAGCAAUUUUCCAGCCGAGCUGCCAGUUAUCUUGAUUAUCUCGUUU
.......((((((...((((.(((((.(((................))).))))).)))).((.((((((((((............))))))))))))................)))))) ( -31.99)
>DroSec_CAF1 1922 120 + 1
UAGUGGGAAGCGAAAAUGGGCAAAUGAAAUUAGCAUUUAUCAAAUUAUGCCAUUUUCCCAAGGACAGCUAGGCUAAGCAAUUUUCCAGCCGAGCUGCCAGCUAUCUUGAUUAUCUCGUUU
(((((((((((.....((((.(((((......((((..........))))))))).)))).((.(((((.((((............)))).))))))).))).)))).))))........ ( -31.00)
>DroSim_CAF1 2026 120 + 1
UAGUGGCAAGCGAAAAUGGGCAAAUGAAAUUACCAUUUAUCAAAUUAUGCCAUUUUCCCAAGGACAGCUAGGCUAAGCAAUUUUCCAGCCGAGCUGCCAGCUAUCUUGAUUAUCUCGUUU
..(((((..(.((((((((.((((((.......))))..........)))))))))).)..((.(((((.((((............)))).))))))).)))))................ ( -29.40)
>DroEre_CAF1 2066 120 + 1
UAGUAGGCAGCGAAAAUAGGCAAAUGAAAUUACCAUUUAUCAAAUUAUGCCAUUUUCCCAAGGACAGCUAGGCUAAGCAAUUUUCCAACCGAGCUGCCUGCUAUCUUGAUUAUCUCGUUU
(((((((((((((((((.((((((((.......))))..........))))))))))....(((..(((......))).....)))......)))))))))))................. ( -32.70)
>DroYak_CAF1 1960 119 + 1
UAGUGGGCAGCAGAAAUAGGCAAAUGAAAUAACCAUUUAUCAAAUUGUGCUGUUUUC-CAAGGACAGCUAGACUAAGCAAUUUUCCAGCCGAGCUGCCAGCUAUCUUGAUUAUCUCGUUU
((((.(((((((....).((((((((.......)))))...((((((((((((((..-...)))))))........)))))))....)))..)))))).))))................. ( -31.20)
>consensus
UAGUGGGAAGCGAAAAUGGGCAAAUGAAAUUACCAUUUAUCAAAUUAUGCCAUUUUCCCAAGGACAGCUAGGCUAAGCAAUUUUCCAGCCGAGCUGCCAGCUAUCUUGAUUAUCUCGUUU
....((..(((((((((.((((((((.......))))..........))))))))))....((.(((((.((((............)))).))))))).)))..)).............. (-22.82 = -22.66 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,959,300 – 5,959,420
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -33.00
Consensus MFE -27.44
Energy contribution -27.24
Covariance contribution -0.20
Combinations/Pair 1.18
Mean z-score -2.31
Structure conservation index 0.83
SVM decision value 2.29
SVM RNA-class probability 0.991771
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5959300 120 - 20766785
AAACGAGAUAAUCAAGAUAACUGGCAGCUCGGCUGGAAAAUUGCUUAGCCAAGCUGUCCUUGGGAAAAUGGAAUAAUUUGAUAAAUGCUAAUUUCAUUUGCCCAUUUUCGUUUCCCACUA
((((((((..............(((((((.((((((........)))))).)))))))..((((.(((((((((................))))))))).)))).))))))))....... ( -35.79)
>DroSec_CAF1 1922 120 - 1
AAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUGAUAAAUGCUAAUUUCAUUUGCCCAUUUUCGCUUCCCACUA
...(((((...(((((((((((((..(((.(((.........))).))))))))))).)))))((((.((((((..........)))))).))))..........))))).......... ( -32.20)
>DroSim_CAF1 2026 120 - 1
AAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUGAUAAAUGGUAAUUUCAUUUGCCCAUUUUCGCUUGCCACUA
...((((....(((((((((((((..(((.(((.........))).))))))))))).)))))((((((((((.....)).(((((((.....))))))).)))))))).))))...... ( -35.00)
>DroEre_CAF1 2066 120 - 1
AAACGAGAUAAUCAAGAUAGCAGGCAGCUCGGUUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUGAUAAAUGGUAAUUUCAUUUGCCUAUUUUCGCUGCCUACUA
..............((.((((.(((((((.((((((........)))))).))))))).....((((((((((.....(((............)))..)))).)))))))))).)).... ( -32.00)
>DroYak_CAF1 1960 119 - 1
AAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGUCUAGCUGUCCUUG-GAAAACAGCACAAUUUGAUAAAUGGUUAUUUCAUUUGCCUAUUUCUGCUGCCCACUA
...........(((((((((((((..(((.(((.........))).))))))))))).))))-)....(((((.((...(.(((((((.....))))))).)...)).)))))....... ( -30.00)
>consensus
AAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUGAUAAAUGGUAAUUUCAUUUGCCCAUUUUCGCUUCCCACUA
...............(..(((.(((((((.((((((........)))))).))))))).....((((((((((.....)).(((((((.....))))))).)))))))))))..)..... (-27.44 = -27.24 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,959,340 – 5,959,450
Length 110
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 95.65
Mean single sequence MFE -31.30
Consensus MFE -28.06
Energy contribution -28.18
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.68
Structure conservation index 0.90
SVM decision value 1.65
SVM RNA-class probability 0.970102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5959340 110 - 20766785
UUGAGUGUCUACUGAAGGGGGUU-UUGUGAUAAACGAGAUAAUCAAGAUAACUGGCAGCUCGGCUGGAAAAUUGCUUAGCCAAGCUGUCCUUGGGAAAAUGGAAUAAUUUG
..((((.((((((.((((..(((-((((.....)))))))..............((((((.((((((........)))))).)))))))))).))....))))...)))). ( -29.70)
>DroSec_CAF1 1962 110 - 1
UUGAGUGUCUGCUGAAGGGGGUU-UUGUGAUAAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUG
....(((((..((.((((..(((-((((.....)))))))..............((((((.((((((........)))))).)))))))))).)).....)))))...... ( -32.60)
>DroSim_CAF1 2066 110 - 1
UUGAGUGUCUGCUGAAGGGGGUU-UUGUGAUAAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUG
....(((((..((.((((..(((-((((.....)))))))..............((((((.((((((........)))))).)))))))))).)).....)))))...... ( -32.60)
>DroEre_CAF1 2106 110 - 1
UUGAGUGUCUGCUGAAGGGGGUU-UUGUGAUAAACGAGAUAAUCAAGAUAGCAGGCAGCUCGGUUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUG
....((((((((((..((..(((-((((.....)))))))..))....)))))(((((((.((((((........)))))).)))))))...........)))))...... ( -31.30)
>DroYak_CAF1 2000 110 - 1
UUGAGUGUCUGCUGAAGGGGGUUUUUGUGAUAAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGUCUAGCUGUCCUUG-GAAAACAGCACAAUUUG
..((((...(((((........((((((.....))))))...(((((((((((((..(((.(((.........))).))))))))))).))))-)....)))))..)))). ( -30.30)
>consensus
UUGAGUGUCUGCUGAAGGGGGUU_UUGUGAUAAACGAGAUAAUCAAGAUAGCUGGCAGCUCGGCUGGAAAAUUGCUUAGCCUAGCUGUCCUUGGGAAAAUGGCAUAAUUUG
....(((((..((.((((.((((.((((.....))))...))))..........((((((.((((((........)))))).)))))))))).)).....)))))...... (-28.06 = -28.18 +   0.12)

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 10:08:23 2006