Locus 3706

Sequence ID 3L_DroMel_CAF1
Location 10,771,894 – 10,772,035
Length 141
Max. P 0.999904
window5790 window5791 window5792 window5793

overview

Window 0

Location 10,771,894 – 10,771,995
Length 101
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 83.55
Mean single sequence MFE -36.34
Consensus MFE -21.00
Energy contribution -22.24
Covariance contribution 1.24
Combinations/Pair 1.17
Mean z-score -3.05
Structure conservation index 0.58
SVM decision value 1.37
SVM RNA-class probability 0.947285
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10771894 101 + 23771897
GUGUUUGCCGCUGAUUGCUUUAAUGGGUCAGCACUGUAC-CAGUUGGGACAUAC---ACAC-------AGAAGUGUGUGUGUGUGUGUUGCACUAACGGUAAACUGGUUUCG
..((((((((((((((.(......)))))))).......-..((((((((((((---((((-------(.(....).))))))))))))...))))))))))))........ ( -38.00)
>DroSec_CAF1 105530 90 + 1
GUGUUUGCCGCUGAUUGCUUUAAUGGGUCACCACUGUAC-CAGUUGGGAC-------ACAC-------AAAAGUGUG----UGUGUGU---GCUAACGGUAAACUGGUUUCG
..(((((((((.....)).......(((((....)).))-).(((((.((-------((((-------(........----)))))))---.))))))))))))........ ( -29.50)
>DroSim_CAF1 108425 100 + 1
GUGUUUGCCGCUGAUUGCUUUAAUGGGUCACCACUGUAC-CAGUUGGGACAUACA-CACAC-------AUAAGUGUGUGUGUGUGUGU---GCUAACGGUAAACUGGUUUCG
..(((((((((.....)).......(((((....)).))-).(((((.(((((((-(((((-------((....))))))))))))))---.))))))))))))........ ( -42.10)
>DroEre_CAF1 110509 106 + 1
GUGUUUGCCGCUGAUUGCUUUAAUGGGUCACCACUGUAC-CAGUUGGGACACAUA-CACGUAUA-UAUGCAAGUGUGUGUGUGUGUGU---GCUAACGGUAAACUGGUUUCG
..(((((((((.....)).......(((((....)).))-).(((((.(((((((-((((((((-(......))))))))))))))))---.))))))))))))........ ( -39.40)
>DroAna_CAF1 106382 106 + 1
GUGUUUGCUGCUGAUUGCUUUAAUGGGUCACCACUGUACCCAGUUGGGACACCCAACACACAUACU--AUAGGUAUGUGCGU-CAUUU---GCCAACGGUAAACUGGUUUCG
..((((((((.((...((.....(((((..((((((....))).)))...)))))((.(((((((.--....))))))).))-.....---)))).))))))))........ ( -32.70)
>consensus
GUGUUUGCCGCUGAUUGCUUUAAUGGGUCACCACUGUAC_CAGUUGGGACACACA_CACAC_______AUAAGUGUGUGUGUGUGUGU___GCUAACGGUAAACUGGUUUCG
..(((((((((..((((...((.(((....))).))....))))..).(((((((.(((((...........))))))))))))............))))))))........ (-21.00 = -22.24 +   1.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,771,894 – 10,771,995
Length 101
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 83.55
Mean single sequence MFE -27.92
Consensus MFE -14.62
Energy contribution -15.66
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.72
Structure conservation index 0.52
SVM decision value 0.60
SVM RNA-class probability 0.796149
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10771894 101 - 23771897
CGAAACCAGUUUACCGUUAGUGCAACACACACACACACACUUCU-------GUGU---GUAUGUCCCAACUG-GUACAGUGCUGACCCAUUAAAGCAAUCAGCGGCAAACAC
........((((.(((((((..(.......(((((((......)-------))))---)).(((.((....)-).))))..)))))........((.....)))).)))).. ( -28.10)
>DroSec_CAF1 105530 90 - 1
CGAAACCAGUUUACCGUUAGC---ACACACA----CACACUUUU-------GUGU-------GUCCCAACUG-GUACAGUGGUGACCCAUUAAAGCAAUCAGCGGCAAACAC
........((((.((((((.(---(((((((----((......)-------))))-------)).((....)-)....))).))))........((.....)))).)))).. ( -22.90)
>DroSim_CAF1 108425 100 - 1
CGAAACCAGUUUACCGUUAGC---ACACACACACACACACUUAU-------GUGUG-UGUAUGUCCCAACUG-GUACAGUGGUGACCCAUUAAAGCAAUCAGCGGCAAACAC
........((((.((((((.(---((..(((((((((......)-------)))))-))).(((.((....)-).)))))).))))........((.....)))).)))).. ( -30.60)
>DroEre_CAF1 110509 106 - 1
CGAAACCAGUUUACCGUUAGC---ACACACACACACACACUUGCAUA-UAUACGUG-UAUGUGUCCCAACUG-GUACAGUGGUGACCCAUUAAAGCAAUCAGCGGCAAACAC
........((((.((((((.(---((....(((((.((((.......-.....)))-).))))).((....)-)....))).))))........((.....)))).)))).. ( -23.30)
>DroAna_CAF1 106382 106 - 1
CGAAACCAGUUUACCGUUGGC---AAAUG-ACGCACAUACCUAU--AGUAUGUGUGUUGGGUGUCCCAACUGGGUACAGUGGUGACCCAUUAAAGCAAUCAGCAGCAAACAC
........((((.(.((((((---....(-((((((((((....--.))))))))))).((.((((((.(((....)))))).)))))......))...)))).).)))).. ( -34.70)
>consensus
CGAAACCAGUUUACCGUUAGC___ACACACACACACACACUUAU_______GUGUG_UGUAUGUCCCAACUG_GUACAGUGGUGACCCAUUAAAGCAAUCAGCGGCAAACAC
........((((.(((((.................(((((...........)))))......((((((.(((....)))))).)))..............))))).)))).. (-14.62 = -15.66 +   1.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,771,933 – 10,772,035
Length 102
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 74.61
Mean single sequence MFE -31.40
Consensus MFE -13.34
Energy contribution -14.86
Covariance contribution 1.52
Combinations/Pair 1.21
Mean z-score -3.56
Structure conservation index 0.42
SVM decision value 4.47
SVM RNA-class probability 0.999904
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10771933 102 + 23771897
CAGUUGGGACAUAC---ACAC-------AGAAGUGUGUGUGUGUGUGUUGCACUAACGGUAAACUGGUUUCGAUGACAUGGCGCAUAACACCCCAGUAUAUAUAUAUAUAUA
....((((((((((---((((-------....))))))))))((((..(((.(((.(((....)))(((.....))).))).)))..))))))))((((((....)))))). ( -33.50)
>DroSec_CAF1 105569 83 + 1
CAGUUGGGAC-------ACAC-------AAAAGUGUG----UGUGUGU---GCUAACGGUAAACUGGUUUCGAUGACAUGGCGCAUAACACCCCAGUAUA--------UAUA
...(((((((-------((((-------....)))))----).(((((---((((.(((....)))(((.....))).)))))))))....)))))....--------.... ( -27.10)
>DroSim_CAF1 108464 93 + 1
CAGUUGGGACAUACA-CACAC-------AUAAGUGUGUGUGUGUGUGU---GCUAACGGUAAACUGGUUUCGAUGACAUGGCGCAUAACACCCCAGUAUA--------UAUA
...((((((((((((-(((((-------....))))))))))))((((---((((.(((....)))(((.....))).)))))))).....)))))....--------.... ( -37.00)
>DroEre_CAF1 110548 99 + 1
CAGUUGGGACACAUA-CACGUAUA-UAUGCAAGUGUGUGUGUGUGUGU---GCUAACGGUAAACUGGUUUCGAUGACAUGGCGCAUAACACCCCAGUAUA--------UAUA
..(((((.(((((((-((((((((-(......))))))))))))))))---.))))).(((.(((((.....(((........)))......))))).))--------)... ( -34.10)
>DroAna_CAF1 106422 91 + 1
CAGUUGGGACACCCAACACACAUACU--AUAGGUAUGUGCGU-CAUUU---GCCAACGGUAAACUGGUUUCGAUGACUACUAGCAUAACAUUCAA---------------CA
..((((((...)))))).(((((((.--....))))))).((-((((.---((((.........))))...))))))..................---------------.. ( -25.30)
>consensus
CAGUUGGGACACACA_CACAC_______AUAAGUGUGUGUGUGUGUGU___GCUAACGGUAAACUGGUUUCGAUGACAUGGCGCAUAACACCCCAGUAUA________UAUA
...((((((((((((.(((((...........))))))))))))((((...((...(((....)))(((.....))).....))...)))))))))................ (-13.34 = -14.86 +   1.52)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,771,933 – 10,772,035
Length 102
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 74.61
Mean single sequence MFE -23.63
Consensus MFE -6.54
Energy contribution -7.30
Covariance contribution 0.76
Combinations/Pair 1.17
Mean z-score -1.80
Structure conservation index 0.28
SVM decision value 0.47
SVM RNA-class probability 0.747446
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10771933 102 - 23771897
UAUAUAUAUAUAUAUACUGGGGUGUUAUGCGCCAUGUCAUCGAAACCAGUUUACCGUUAGUGCAACACACACACACACACUUCU-------GUGU---GUAUGUCCCAACUG
((((((....)))))).((((((((..(((((.(((....(.......).....)))..)))))..))))(((.((((((....-------))))---)).))))))).... ( -24.20)
>DroSec_CAF1 105569 83 - 1
UAUA--------UAUACUGGGGUGUUAUGCGCCAUGUCAUCGAAACCAGUUUACCGUUAGC---ACACACA----CACACUUUU-------GUGU-------GUCCCAACUG
....--------((.(((((((((.....)))).((....))...))))).))..(((.(.---(((((((----........)-------))))-------)).).))).. ( -20.30)
>DroSim_CAF1 108464 93 - 1
UAUA--------UAUACUGGGGUGUUAUGCGCCAUGUCAUCGAAACCAGUUUACCGUUAGC---ACACACACACACACACUUAU-------GUGUG-UGUAUGUCCCAACUG
....--------((.(((((((((.....)))).((....))...))))).))..(((.(.---(((.(((((((((......)-------)))))-))).))).).))).. ( -27.30)
>DroEre_CAF1 110548 99 - 1
UAUA--------UAUACUGGGGUGUUAUGCGCCAUGUCAUCGAAACCAGUUUACCGUUAGC---ACACACACACACACACUUGCAUA-UAUACGUG-UAUGUGUCCCAACUG
....--------((.(((((((((.....)))).((....))...))))).))..(((.(.---(((((.((((.............-.....)))-).))))).).))).. ( -20.57)
>DroAna_CAF1 106422 91 - 1
UG---------------UUGAAUGUUAUGCUAGUAGUCAUCGAAACCAGUUUACCGUUGGC---AAAUG-ACGCACAUACCUAU--AGUAUGUGUGUUGGGUGUCCCAACUG
.(---------------(((((((.((.(((.((..........)).))).)).))))(((---(..((-((((((((((....--.))))))))))))..)))).)))).. ( -25.80)
>consensus
UAUA________UAUACUGGGGUGUUAUGCGCCAUGUCAUCGAAACCAGUUUACCGUUAGC___ACACACACACACACACUUAU_______GUGUG_UGUAUGUCCCAACUG
.................((((((((...((.....((...(.......)...)).....))...)))).......(((((...........)))))........)))).... ( -6.54 =  -7.30 +   0.76)

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 11:04:50 2006