Locus 461

Sequence ID 2R_DroMel_CAF1
Location 2,626,209 – 2,626,337
Length 128
Max. P 0.994922
window880 window881 window882 window883

overview

Window 0

Location 2,626,209 – 2,626,313
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 88.45
Mean single sequence MFE -31.07
Consensus MFE -25.85
Energy contribution -25.63
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -3.00
Structure conservation index 0.83
SVM decision value 1.33
SVM RNA-class probability 0.943191
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2626209 104 + 20766785
GGUUUCGCCCCACAUGCCCCACAUGCCGCAUGCCGCAUGCAGCAUGCAACCAGCAAUAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACU
((((........((((.....))))..((((((.(....).)))))))))).......(((...((((..((((((.......))))))...))))..)))... ( -33.20)
>DroSec_CAF1 60779 88 + 1
GGUUUCGCCCCACAU---------GC-------CGCAUGCAGCAUGCAACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACU
......((.....((---------((-------.(((((..(((((..........)))))..)))))..((((((.......))))))...))))..)).... ( -28.40)
>DroSim_CAF1 58294 95 + 1
GGUUUCGCCCCACAU---------GCCGCUUGCCGCAUGCAGCAUGCAACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACU
(((............---------)))((((((.(((((..(((((..........)))))..)))))..((((((.......))))))...)))..))).... ( -31.60)
>consensus
GGUUUCGCCCCACAU_________GCCGC_UGCCGCAUGCAGCAUGCAACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACU
((.....))...............((........(((((..(((((..........)))))..)))))..((((((.......))))))...)).......... (-25.85 = -25.63 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,626,209 – 2,626,313
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 88.45
Mean single sequence MFE -44.03
Consensus MFE -31.93
Energy contribution -32.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.78
Structure conservation index 0.73
SVM decision value 1.10
SVM RNA-class probability 0.915477
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2626209 104 - 20766785
AGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUAUUGCUGGUUGCAUGCUGCAUGCGGCAUGCGGCAUGUGGGGCAUGUGGGGCGAAACC
..(((((........((((((.......))))))(..((((((.(((((.....(((((((((((....)))))))))))))))).))))))..)))))).... ( -46.80)
>DroSec_CAF1 60779 88 - 1
AGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUUGCAUGCUGCAUGCG-------GC---------AUGUGGGGCGAAACC
..(((((........((((((.......))))))(..((((((((((((.((((....)).)).)))))))-------))---------)))..)))))).... ( -39.00)
>DroSim_CAF1 58294 95 - 1
AGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUUGCAUGCUGCAUGCGGCAAGCGGC---------AUGUGGGGCGAAACC
..(((((.((((...((((((.......))))))..)))).(..(((((((((.((((((((...)))))))).))))))---------)))..)))))).... ( -46.30)
>consensus
AGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUUGCAUGCUGCAUGCGGCA_GCGGC_________AUGUGGGGCGAAACC
..(((((..(((...((((((.......))))))..((((((.((((((........)))))).)))))).....................))).))))).... (-31.93 = -32.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,626,233 – 2,626,337
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 83.25
Mean single sequence MFE -30.82
Consensus MFE -21.42
Energy contribution -21.82
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.34
Structure conservation index 0.69
SVM decision value 2.52
SVM RNA-class probability 0.994922
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2626233 104 + 20766785
GCCGCAUGCCGCAUGCAGCAUGCAACCAGCAAUAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACUUGCUCUAAAAUCUCAACUGCGAGU
((.(.((((.(((((..((((((.....)))...)))..)))))..((((((.......))))))...))))).)).((((((...............)))))) ( -35.36)
>DroSec_CAF1 60794 97 + 1
GC-------CGCAUGCAGCAUGCAACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACUUGCUCCAAAAUCGCAACUGAGAGU
((-------.(((((..(((((..........)))))..)))))..((((((.......))))))...)).((((....((((.........)))))))).... ( -30.40)
>DroSim_CAF1 58309 104 + 1
GCCGCUUGCCGCAUGCAGCAUGCAACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACUUGCUCCAAAAUCGCAACUGCGAGU
...((((((.(((((..(((((..........)))))..)))))..((((((.......))))))...)))..))).((((((...............)))))) ( -35.26)
>DroEre_CAF1 59789 104 + 1
GCCACCAGCCACCAGCCACCAGCCACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAGCAGCAUCAGCAACUUGCUCCCAAAUCGCAACUGCCAGU
.......((.....((.....))....(((((..(((...((((..((((((.......))))))...))))..)))..)))))........)).......... ( -25.00)
>DroYak_CAF1 58238 85 + 1
-------------------AUGCAACUAGCAACAUGCAACUAGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACUUGCUCCCAAAUCGCAUCUGCUAGU
-------------------.....(((((((..((((.....((..((((((.......))))))...))...(((.....)))........)))).))))))) ( -28.10)
>consensus
GCC_C__GCCGCAUGCAGCAUGCAACCAGCAACAUGCAACAUGCAAUGCCGCGACAUUAGCGGCAACAGCAUCAGCAACUUGCUCCAAAAUCGCAACUGCGAGU
...........................(((((..(((...((((..((((((.......))))))...))))..)))..))))).................... (-21.42 = -21.82 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,626,233 – 2,626,337
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 83.25
Mean single sequence MFE -41.20
Consensus MFE -28.62
Energy contribution -30.74
Covariance contribution 2.12
Combinations/Pair 1.07
Mean z-score -3.30
Structure conservation index 0.69
SVM decision value 2.48
SVM RNA-class probability 0.994489
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2626233 104 - 20766785
ACUCGCAGUUGAGAUUUUAGAGCAAGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUAUUGCUGGUUGCAUGCUGCAUGCGGCAUGCGGC
.((((....)))).......(((((..(((..((((...((((((.......))))))..))))...)))..))))).(((((((((((....))))))))))) ( -44.10)
>DroSec_CAF1 60794 97 - 1
ACUCUCAGUUGCGAUUUUGGAGCAAGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUUGCAUGCUGCAUGCG-------GC
.......((((((((.((((.((((...((....))..))))..)))).)))))))).((((((((.((((((........)))))).)))))))-------). ( -39.20)
>DroSim_CAF1 58309 104 - 1
ACUCGCAGUUGCGAUUUUGGAGCAAGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUUGCAUGCUGCAUGCGGCAAGCGGC
..((((.((((((((.((((.((((...((....))..))))..)))).)))))))).((((((((.((((((........)))))).))))))))...)))). ( -43.90)
>DroEre_CAF1 59789 104 - 1
ACUGGCAGUUGCGAUUUGGGAGCAAGUUGCUGAUGCUGCUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUGGCUGGUGGCUGGUGGCUGGUGGC
...((((((.((((((((....))))))))....))))))(((((((.....(((((((...)))))))..((..(..((.(....).))..)..))))))))) ( -45.30)
>DroYak_CAF1 58238 85 - 1
ACUAGCAGAUGCGAUUUGGGAGCAAGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCUAGUUGCAUGUUGCUAGUUGCAU-------------------
((((((((((((((((....(((((...((....))...((((((.......))))))))))))))))))).)))))))).....------------------- ( -33.50)
>consensus
ACUCGCAGUUGCGAUUUUGGAGCAAGUUGCUGAUGCUGUUGCCGCUAAUGUCGCGGCAUUGCAUGUUGCAUGUUGCUGGUUGCAUGCUGCAUGCGGC__G_GGC
....((((((((((((....(((((..(((..((((...((((((.......))))))..))))...)))..)))))))))))).))))).............. (-28.62 = -30.74 +   2.12)

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 09:39:12 2006