Locus 2562

Sequence ID 3L_DroMel_CAF1
Location 7,169,724 – 7,169,814
Length 90
Max. P 0.711515
window3972 window3973

overview

Window 2

Location 7,169,724 – 7,169,814
Length 90
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -25.14
Consensus MFE -12.52
Energy contribution -12.52
Covariance contribution 0.00
Combinations/Pair 1.20
Mean z-score -2.04
Structure conservation index 0.50
SVM decision value 0.38
SVM RNA-class probability 0.711515
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7169724 90 + 23771897
AUACUU--GGCUC---GCAGGAGAUUC---ACACAUGUAACAAAGCACGGAACCAACAAAAUAUCCUGG-GACCAGAAUAAUGGUCCAUCGUGCUGCCC---------
......--(((..---(((........---.....))).....(((((((......((........))(-(((((......)))))).)))))))))).--------- ( -23.22)
>DroSec_CAF1 32380 90 + 1
AUACUU--GGCUA---GCAGGAGAUUC---ACACAUGUAACAAAGCACGGAACCAACAAAAUAUCCUGG-GACCAGGAUAAUGGUCCAGCGUGCUGCCC---------
......--(((.(---(((.(......---.....(((......))).(((.(((......(((((((.-...))))))).))))))..).))))))).--------- ( -26.10)
>DroSim_CAF1 32773 90 + 1
AUACUU--GGCUA---GCAGGAGAUUC---ACACAUGUAACAAAGCACGGAACCAACAAAAUAUCCUGG-GACCAGGAUAAUGGUCCAUCGUGCUGCCC---------
......--(((.(---(((.((.....---.....(((......))).(((.(((......(((((((.-...))))))).)))))).)).))))))).--------- ( -27.80)
>DroEre_CAF1 37298 90 + 1
AUACUU--GGGUA---GCAGCAGAUUC---ACACAUGUAACAAAGCAUCGAACGAACAAAAUAUCCUGG-GACCAGGAUAAUGCUCCAUCGUGUUGCCC---------
......--(((((---((((((.....---.....))).....((((((....))......(((((((.-...))))))).))))......))))))))--------- ( -23.80)
>DroYak_CAF1 35547 102 + 1
AUACUU--GGGUA---GCAGCAGAUUCUGCUCACAUGUAACAAAGCAUCGAAAGAACAAAAUAUCCUGG-GACCAGGAUAAUGCUCCAUCGUGUUGCCCCGUUUUUUU
......--(((((---(((((((...)))).............((((((....))......(((((((.-...))))))).))))......))))))))......... ( -31.40)
>DroPer_CAF1 42872 81 + 1
GUACUCCCAAGAAGGGGCAAGAUUUUC---ACACAUGUAACAAAGCAU---------------UUCUGGCAGCCAGGAUAAUGGGCCAUCGGCUUGCCU---------
......((.....))((((((......---....((((......))))---------------...((((..(((......)))))))....)))))).--------- ( -18.50)
>consensus
AUACUU__GGCUA___GCAGGAGAUUC___ACACAUGUAACAAAGCACGGAACCAACAAAAUAUCCUGG_GACCAGGAUAAUGGUCCAUCGUGCUGCCC_________
................((((...............(((......)))..............((((((((...)))))))).............))))........... (-12.52 = -12.52 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,169,724 – 7,169,814
Length 90
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.85
Mean single sequence MFE -29.42
Consensus MFE -11.14
Energy contribution -11.39
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -2.32
Structure conservation index 0.38
SVM decision value -0.05
SVM RNA-class probability 0.507752
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7169724 90 - 23771897
---------GGGCAGCACGAUGGACCAUUAUUCUGGUC-CCAGGAUAUUUUGUUGGUUCCGUGCUUUGUUACAUGUGU---GAAUCUCCUGC---GAGCC--AAGUAU
---------.(((((((((..((((((.(((((((...-.)))))))......))))))))))))...((((....))---)).........---..)))--...... ( -28.60)
>DroSec_CAF1 32380 90 - 1
---------GGGCAGCACGCUGGACCAUUAUCCUGGUC-CCAGGAUAUUUUGUUGGUUCCGUGCUUUGUUACAUGUGU---GAAUCUCCUGC---UAGCC--AAGUAU
---------.(((((((((..((((((.(((((((...-.)))))))......))))))))))))...((((....))---)).........---..)))--...... ( -31.50)
>DroSim_CAF1 32773 90 - 1
---------GGGCAGCACGAUGGACCAUUAUCCUGGUC-CCAGGAUAUUUUGUUGGUUCCGUGCUUUGUUACAUGUGU---GAAUCUCCUGC---UAGCC--AAGUAU
---------.(((((((((..((((((.(((((((...-.)))))))......))))))))))))...((((....))---)).........---..)))--...... ( -31.50)
>DroEre_CAF1 37298 90 - 1
---------GGGCAACACGAUGGAGCAUUAUCCUGGUC-CCAGGAUAUUUUGUUCGUUCGAUGCUUUGUUACAUGUGU---GAAUCUGCUGC---UACCC--AAGUAU
---------(((.....(((..(((((.(((((((...-.)))))))...)))))..)))..((....((((....))---))....))...---..)))--...... ( -27.90)
>DroYak_CAF1 35547 102 - 1
AAAAAAACGGGGCAACACGAUGGAGCAUUAUCCUGGUC-CCAGGAUAUUUUGUUCUUUCGAUGCUUUGUUACAUGUGAGCAGAAUCUGCUGC---UACCC--AAGUAU
.....(((((((((...(((.((((((.(((((((...-.)))))))...)))))).))).)))))))))((.((.((((((......))))---).).)--).)).. ( -37.20)
>DroPer_CAF1 42872 81 - 1
---------AGGCAAGCCGAUGGCCCAUUAUCCUGGCUGCCAGAA---------------AUGCUUUGUUACAUGUGU---GAAAAUCUUGCCCCUUCUUGGGAGUAC
---------.((((.((((((((....)))))..)))))))....---------------........((((....))---))......((((((.....))).))). ( -19.80)
>consensus
_________GGGCAACACGAUGGACCAUUAUCCUGGUC_CCAGGAUAUUUUGUUGGUUCCAUGCUUUGUUACAUGUGU___GAAUCUCCUGC___UACCC__AAGUAU
.........(((((..............((((((((...))))))))..............))))).......................................... (-11.14 = -11.39 +   0.25)

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 10:35:41 2006