Locus 6012

Sequence ID 3L_DroMel_CAF1
Location 16,044,293 – 16,044,445
Length 152
Max. P 0.958047
window9615 window9616 window9617

overview

Window 5

Location 16,044,293 – 16,044,413
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.74
Mean single sequence MFE -24.36
Consensus MFE -19.22
Energy contribution -20.22
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.79
SVM decision value 1.48
SVM RNA-class probability 0.958047
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16044293 120 + 23771897
CGUUAUAUCGUUUCUAUUAGAACUGGAAAAGCAUCGAUGUUUUUGCCAGGCCAACAUCAAUAACCAAUAAUCAUCGAUGUUUUUCUUGCUCCUGGUUCGUUACAAUACAAUACUAAACAC
.........((((.((((.((((((((((((((((((((...(((...((.............))..))).))))))))))))))).......)))))((......))))))..)))).. ( -23.43)
>DroSec_CAF1 14709 105 + 1
CGUUUUAUCGUUUCUAUUAGAACUAGAAAAGCAUCGAUGUUUUUGCCAGGACUACAUCGAUAACCAAUAAUCAUCGAUAUUUUUCUUGCUCCUGGUUCGUUA---------------CAC
...................((((((((((((((....)))))))((.((((..(.((((((...........)))))).)..)))).))..)))))))....---------------... ( -20.80)
>DroSim_CAF1 12215 120 + 1
CGUUUUAUCGUUUCUAUUAGAACUAGAAAAGCAUCGAUGUUUUUGCCAGGACUACAUCGAUAACCAAUAAUCAUCGAUGUUUUUCUUGCUCCUGGUUCGUUACAAUACAAUACUUAACAC
.(((.(((.((........((((((((((((((....)))))))((.((((..((((((((...........))))))))..)))).))..)))))))........)).)))...))).. ( -28.19)
>DroEre_CAF1 14676 116 + 1
CGUUAUAUCGUUUCUCUUAGAACUGGAAAAUCAUCGAUGUUUUUGC-AGGUAAACAUCGAUAGCCAAUAAUCAUCGAUGUUUUUCUUGCUUCUAUUUCGUUAC--U-CAAUACUUAACAC
.((((............((((((.((((((.((((((((...(((.-.(((...........)))..))).)))))))).)))))).).)))))....((...--.-....)).)))).. ( -22.90)
>DroYak_CAF1 37150 114 + 1
CGUUAUAUCGUUUCUAUUAGAACUGGAAAAGCAUCGAUGUUUUUGC-AGGUAAACAUCGAUAACCAAUAAUCAUCGAUGUUUUUCUUGCUUCUGUUUCGUUAC--UACAAUACAUAA---
.((..((.((.......((((((.(((((((((((((((...(((.-.(((...........)))..))).))))))))))))))).).)))))...)).)).--.)).........--- ( -26.50)
>consensus
CGUUAUAUCGUUUCUAUUAGAACUGGAAAAGCAUCGAUGUUUUUGCCAGGACAACAUCGAUAACCAAUAAUCAUCGAUGUUUUUCUUGCUCCUGGUUCGUUAC__UACAAUACUUAACAC
...................((((((((((((((....)))))))((.(((..(((((((((...........)))))))))..))).))..)))))))...................... (-19.22 = -20.22 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,044,293 – 16,044,413
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.74
Mean single sequence MFE -26.08
Consensus MFE -17.98
Energy contribution -18.66
Covariance contribution 0.68
Combinations/Pair 1.08
Mean z-score -1.80
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.566808
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16044293 120 - 23771897
GUGUUUAGUAUUGUAUUGUAACGAACCAGGAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUUGAUGUUGGCCUGGCAAAAACAUCGAUGCUUUUCCAGUUCUAAUAGAAACGAUAUAACG
..........(((((((((..(......(((((..(((((.((((((((......(((((.......))))).........)))))))).)))))..)))))....)..))))))))).. ( -28.46)
>DroSec_CAF1 14709 105 - 1
GUG---------------UAACGAACCAGGAGCAAGAAAAAUAUCGAUGAUUAUUGGUUAUCGAUGUAGUCCUGGCAAAAACAUCGAUGCUUUUCUAGUUCUAAUAGAAACGAUAAAACG
...---------------..........(((((.((((((.((((((((..(((((.....)))))..((....)).....)))))))).)))))).))))).................. ( -23.20)
>DroSim_CAF1 12215 120 - 1
GUGUUAAGUAUUGUAUUGUAACGAACCAGGAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUCGAUGUAGUCCUGGCAAAAACAUCGAUGCUUUUCUAGUUCUAAUAGAAACGAUAAAACG
..(((((((((((...(((......((((((.........(((((((((((.....)))))))))))..)))))).....))).))))))))(((((.......))))).......))). ( -30.30)
>DroEre_CAF1 14676 116 - 1
GUGUUAAGUAUUG-A--GUAACGAAAUAGAAGCAAGAAAAACAUCGAUGAUUAUUGGCUAUCGAUGUUUACCU-GCAAAAACAUCGAUGAUUUUCCAGUUCUAAGAGAAACGAUAUAACG
..(((..((((((-.--.(..(....(((((.(..(((((.((((((((.........))))(((((((....-....))))))))))).)))))..)))))).)..)..))))))))). ( -20.60)
>DroYak_CAF1 37150 114 - 1
---UUAUGUAUUGUA--GUAACGAAACAGAAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUCGAUGUUUACCU-GCAAAAACAUCGAUGCUUUUCCAGUUCUAAUAGAAACGAUAUAACG
---...(((((((((--(((.(((.......(((.(..(((((((((((((.....)))))))))))))..))-)).......))).)))).......(((.....)))))))))))... ( -27.84)
>consensus
GUGUUAAGUAUUGUA__GUAACGAACCAGGAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUCGAUGUUGACCUGGCAAAAACAUCGAUGCUUUUCCAGUUCUAAUAGAAACGAUAUAACG
............................(((((..(((((.((((((((((.....))))))((((((...........)))))))))).)))))..))))).................. (-17.98 = -18.66 +   0.68)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,044,333 – 16,044,445
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 84.89
Mean single sequence MFE -23.54
Consensus MFE -16.00
Energy contribution -16.28
Covariance contribution 0.28
Combinations/Pair 1.11
Mean z-score -1.88
Structure conservation index 0.68
SVM decision value 0.25
SVM RNA-class probability 0.652556
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16044333 112 - 23771897
UAUCCAUAUAAUUUUUUUAACGACAUCGAAGUGUGUUUAGUAUUGUAUUGUAACGAACCAGGAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUUGAUGUUGGCCUGGCAAAA
.....(((((((......(((.((((....)))))))....))))))).........(((((.........((((((((((((.....))))))))))))..)))))..... ( -23.70)
>DroSec_CAF1 14749 97 - 1
UAUCCAUAUAAUAUGAUUAACGACAUCGAAAUGUG---------------UAACGAACCAGGAGCAAGAAAAAUAUCGAUGAUUAUUGGUUAUCGAUGUAGUCCUGGCAAAA
....(((((....((((.......))))..)))))---------------.......((((((.........(((((((((((.....)))))))))))..))))))..... ( -18.80)
>DroSim_CAF1 12255 112 - 1
UAUCCAUAUAAUAUGUUUAACGACAUCGAAGUGUGUUAAGUAUUGUAUUGUAACGAACCAGGAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUCGAUGUAGUCCUGGCAAAA
.....(((((((((..(((((.((((....)))))))))))))))))).........((((((.........(((((((((((.....)))))))))))..))))))..... ( -29.00)
>DroEre_CAF1 14716 108 - 1
UAUCCAUAUAAUAGGUUUAACGACAUCGAGGUGUGUUAAGUAUUG-A--GUAACGAAAUAGAAGCAAGAAAAACAUCGAUGAUUAUUGGCUAUCGAUGUUUACCU-GCAAAA
........(((((..((((((.((((....)))))))))))))))-.--..............(((.(..(((((((((((.........)))))))))))..))-)).... ( -21.60)
>DroYak_CAF1 37190 105 - 1
UAUCCAUAUAAUAUUUUUAACGACAUCGAAG----UUAUGUAUUGUA--GUAACGAAACAGAAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUCGAUGUUUACCU-GCAAAA
......((((((((...((((.........)----))).))))))))--..............(((.(..(((((((((((((.....)))))))))))))..))-)).... ( -24.60)
>consensus
UAUCCAUAUAAUAUGUUUAACGACAUCGAAGUGUGUUAAGUAUUGUA__GUAACGAACCAGGAGCAAGAAAAACAUCGAUGAUUAUUGGUUAUCGAUGUUGACCUGGCAAAA
....................((....))...................................((.((...((((((((((((.....))))))))))))...)).)).... (-16.00 = -16.28 +   0.28)

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 12:06:45 2006