Locus 623

Sequence ID 2R_DroMel_CAF1
Location 3,147,141 – 3,147,289
Length 148
Max. P 0.908621
window1114 window1115 window1116

overview

Window 4

Location 3,147,141 – 3,147,249
Length 108
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -35.93
Consensus MFE -27.49
Energy contribution -28.27
Covariance contribution 0.78
Combinations/Pair 1.17
Mean z-score -3.02
Structure conservation index 0.76
SVM decision value 1.02
SVM RNA-class probability 0.902057
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3147141 108 + 20766785
GCAACAUUUGUUGCGG-GCUGACAACCGAUAACUCAAAGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGUCU--GCUGUUUGUUUUGUUUG
(((((....)))))((-........)).......(((((((.((((((((.(((((((((....)))))))))))))))((((.....))))--...)).))))))).... ( -36.60)
>DroSec_CAF1 36892 108 + 1
GCAACAUUUGUUGCGG-GCUGGCGAACGAUAAGUCAAAGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAUACUUUCUGCCU--CCUGUUUGUUUUGUUUG
(((((....)))))((-((.(((((((((....))...(((........(((((((((((....)))))))))))((((....)))))))..--...)))))))..)))). ( -33.30)
>DroSim_CAF1 37760 106 + 1
GCAACAUUUGUUGCGG-GCUGGCGAACGAUAAGC--AAGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGCCU--CCUGUUUGUUUUGUUUG
(((((....)))))((-((.((((((((....((--(......(((((.(((((((((((....))))))))))).)))))......)))..--..))))))))..)))). ( -37.50)
>DroEre_CAF1 36694 106 + 1
GCAACAUUUGUUGCUG-GCUAGUGAACCCGAAGUCGAAGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCCGAAAAGACUUUCUGUCU--AU--UUUGUUUUGUUUG
(((((....))))).(-(((..((....)).))))((((((........(((((((((((....)))))))))))....((((.....))))--..--..))))))..... ( -34.90)
>DroYak_CAF1 37284 106 + 1
GCAACAUUUGUUGCUG-GCCGGUGAGCGAUAAGUCGAAGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGUCU--AU--UUAGUUUUGUUUG
.....((((((((((.-(....).))))))))))((((((.........(((((((((((....)))))))))))(((.((((.....))))--.)--)).)))))).... ( -35.50)
>DroAna_CAF1 35863 102 + 1
GCAACAUUUGUUGCUUCGCCCGCAAA---------AAAGCAUACUUUUAGGCGAGCUUUCGUGAGGGAGCUUGCUGGAAAGUCUUUCUGUGUUGCCAUUUUGUGUUGUUCG
(((((....)))))......((((((---------(.(((((((((((.((((((((..(....)..)))))))).))))))......)))))....)))))))....... ( -37.80)
>consensus
GCAACAUUUGUUGCGG_GCUGGCGAACGAUAAGUCAAAGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGUCU__CCUGUUUGUUUUGUUUG
(((((....)))))....................(((((((..(((((.(((((((((((....))))))))))).))))).(.....)...........))))))).... (-27.49 = -28.27 +   0.78)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,147,141 – 3,147,249
Length 108
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.52
Mean single sequence MFE -26.32
Consensus MFE -17.67
Energy contribution -18.50
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -2.41
Structure conservation index 0.67
SVM decision value 0.27
SVM RNA-class probability 0.662020
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3147141 108 - 20766785
CAAACAAAACAAACAGC--AGACAGAAAGUCUUUUCAGCAAGCUCUCACCUGAAAGCUUGCCUAAAAGUAUGCUUUGAGUUAUCGGUUGUCAGC-CCGCAACAAAUGUUGC
...............((--.(((((((((((((((..(((((((.((....)).)))))))..)))))...)))))((....))..))))).))-..(((((....))))) ( -28.60)
>DroSec_CAF1 36892 108 - 1
CAAACAAAACAAACAGG--AGGCAGAAAGUAUUUUCAGCAAGCUCUCACCUGAAAGCUUGCCUAAAAGUAUGCUUUGACUUAUCGUUCGCCAGC-CCGCAACAAAUGUUGC
...............((--.(((..((((((((((..(((((((.((....)).)))))))..)))...)))))))(((.....))).)))...-))(((((....))))) ( -26.80)
>DroSim_CAF1 37760 106 - 1
CAAACAAAACAAACAGG--AGGCAGAAAGUCUUUUCAGCAAGCUCUCACCUGAAAGCUUGCCUAAAAGUAUGCUU--GCUUAUCGUUCGCCAGC-CCGCAACAAAUGUUGC
.......(((....((.--(((((......(((((..(((((((.((....)).)))))))..)))))..)))))--.))....))).......-..(((((....))))) ( -27.30)
>DroEre_CAF1 36694 106 - 1
CAAACAAAACAAA--AU--AGACAGAAAGUCUUUUCGGCAAGCUCUCACCUGAAAGCUUGCCUAAAAGUAUGCUUCGACUUCGGGUUCACUAGC-CAGCAACAAAUGUUGC
.............--..--.....(((.(((((((.((((((((.((....)).)))))))).))))).))..))).......(((......))-).(((((....))))) ( -28.70)
>DroYak_CAF1 37284 106 - 1
CAAACAAAACUAA--AU--AGACAGAAAGUCUUUUCAGCAAGCUCUCACCUGAAAGCUUGCCUAAAAGUAUGCUUCGACUUAUCGCUCACCGGC-CAGCAACAAAUGUUGC
.............--..--.....(((((((......(((((((.((....)).)))))))....(((....))).))))).))(((....)))-..(((((....))))) ( -23.40)
>DroAna_CAF1 35863 102 - 1
CGAACAACACAAAAUGGCAACACAGAAAGACUUUCCAGCAAGCUCCCUCACGAAAGCUCGCCUAAAAGUAUGCUUU---------UUUGCGGGCGAAGCAACAAAUGUUGC
((............((....))..((..(((((......))).))..)).))...((((((..(((((....))))---------)..))))))...(((((....))))) ( -23.10)
>consensus
CAAACAAAACAAACAGG__AGACAGAAAGUCUUUUCAGCAAGCUCUCACCUGAAAGCUUGCCUAAAAGUAUGCUUUGACUUAUCGUUCGCCAGC_CAGCAACAAAUGUUGC
..........................(((((((((..(((((((.((....)).)))))))..)))))...))))......................(((((....))))) (-17.67 = -18.50 +   0.83)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,147,177 – 3,147,289
Length 112
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 84.60
Mean single sequence MFE -27.32
Consensus MFE -23.34
Energy contribution -23.45
Covariance contribution 0.11
Combinations/Pair 1.18
Mean z-score -2.28
Structure conservation index 0.85
SVM decision value 1.06
SVM RNA-class probability 0.908621
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3147177 112 + 20766785
AGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGUCU--GCUGUUUGUUUUGUUUGCUCAUUAACCGAUAUUUGCACCCCUAUUUGACACACACAC
((((...((((.(((((((((((....))))))))))).))))(((.....))))--)))((.((((..((.(((..((........))..))).....))..)))).)).... ( -27.80)
>DroSec_CAF1 36928 112 + 1
AGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAUACUUUCUGCCU--CCUGUUUGUUUUGUUUGCUCAUUAACCGAUAUUUGCACCCCUAUUUGACACACACAC
.(((........(((((((((((....)))))))))))((((....)))))))..--..(((.((((..((.(((..((........))..))).....))..)))).)))... ( -24.00)
>DroSim_CAF1 37794 112 + 1
AGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGCCU--CCUGUUUGUUUUGUUUGCUCAUUAACCGAUAUUUGCACCCCUAUUUGACACACACAC
.(((..(((((.(((((((((((....))))))))))).)))))...........--..((((.(((.((......))..))).))))..)))..................... ( -25.80)
>DroEre_CAF1 36730 98 + 1
AGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCCGAAAAGACUUUCUGUCU--AU--UUUGUUUUGUUUGCUCAUUAACCGAUAUUUGCACCCC--------ACAC----
((((.((.....(((((((((((....)))))))))))((((((((.....))))--.)--))).....)).))))......................--------....---- ( -28.00)
>DroYak_CAF1 37320 98 + 1
AGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGUCU--AU--UUAGUUUUGUUUGCUCAUUAACCGAUAUUUGCACCCC--------ACAC----
((((.((.....(((((((((((....)))))))))))(((.((((.....))))--.)--))......)).))))......................--------....---- ( -25.60)
>DroAna_CAF1 35891 102 + 1
AGCAUACUUUUAGGCGAGCUUUCGUGAGGGAGCUUGCUGGAAAGUCUUUCUGUGUUGCCAUUUUGUGUUGUUCGCUCAUUAACAAAUAUUUGCACACCU--------CA----C
.....((((((.((((((((..(....)..)))))))).)))))).....(((((......(((((..((......))...))))).....)))))...--------..----. ( -32.70)
>consensus
AGCAUACUUUUAGGCAAGCUUUCAGGUGAGAGCUUGCUGAAAAGACUUUCUGUCU__CCUGUUUGUUUUGUUUGCUCAUUAACCGAUAUUUGCACCCCU_______ACAC___C
.(((..(((((.(((((((((((....))))))))))).))))).........................(((........))).......)))..................... (-23.34 = -23.45 +   0.11)

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 09:43:02 2006