Locus 495

Sequence ID 2R_DroMel_CAF1
Location 2,718,055 – 2,718,232
Length 177
Max. P 0.974451
window940 window941 window942 window943 window944

overview

Window 0

Location 2,718,055 – 2,718,156
Length 101
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 88.00
Mean single sequence MFE -28.71
Consensus MFE -23.48
Energy contribution -23.72
Covariance contribution 0.24
Combinations/Pair 1.11
Mean z-score -2.05
Structure conservation index 0.82
SVM decision value 1.39
SVM RNA-class probability 0.949342
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2718055 101 - 20766785
UUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGCUC-----AGAUAUAUACCUGCUAAUACCUAUGUAUCCGCAGCGAAA
...((((((((((....))))))))))...(((((....(((((((.....-----....)))))))-----.)))))...(((((..((((....))))..)))).)... ( -29.70)
>DroSec_CAF1 9619 99 - 1
UUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGCUC-----AGAU--AUACCUGCUAAUACCUAUGUAUCCGCAGCGAAA
...((((((((((....))))))))))...(((((....(((((((.....-----....)))))))-----.)))--)).(((((..((((....))))..)))).)... ( -29.70)
>DroEre_CAF1 1245 99 - 1
U-UCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGUUC-----GGAUAUAUACCUGCU-AUACUCAUGUAUCCGCAGCGAAA
.-.((((((((((....))))))))))......((....))..........-----.....((((((-----((((((((.......-......))))))))).))))).. ( -27.52)
>DroYak_CAF1 9900 101 - 1
UUUCUGAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGCUC-----AGAUAUAUACCUGCUAAUACUUAUGUGUCUGCAGCGAAA
...((.(((((((....))))))).))...(((((....(((((((.....-----....)))))))-----.)))))...(((((..((((....))))..)))).)... ( -28.60)
>DroAna_CAF1 9312 111 - 1
UUUCUCAAGUCAUUUGUGUGAUUUGGGUUUAUGUCGGAAGAGCGGCAGCAGCCGAAAAUAAUCGUAUAUGGUAUAUAUAAACCUGCUAAUACAUAUGUAUCCACAGCGAAA
...((((((((((....))))))))))......((....)).((((....)))).......((((...(((.(((((((..............))))))))))..)))).. ( -28.04)
>consensus
UUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG_____AAUAAUCGCUC_____AGAUAUAUACCUGCUAAUACCUAUGUAUCCGCAGCGAAA
...((((((((((....))))))))))......(((...(((((((..............)))))))...............((((..((((....))))..))))))).. (-23.48 = -23.72 +   0.24) 

alignment

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secondary structure

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Window 1

Location 2,718,086 – 2,718,196
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -23.24
Consensus MFE -17.97
Energy contribution -18.47
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.77
SVM decision value 1.73
SVM RNA-class probability 0.974451
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2718086 110 + 20766785
AUAUAUCU-----GAGCGAUUAUU-----CUUCCACCGCUCUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCCAACCUUU
........-----(((((......-----.......)))))............((((((((((.(((.....)))........((((.....))))....)))))))))).......... ( -27.82)
>DroPse_CAF1 9326 86 + 1
----------------------------------ACAGAAAUGUCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGAGGCUAACCUUU
----------------------------------(((....))).....(((.((((((((((.(((.....)))........((((.....))))....)))))))).)).)))..... ( -18.80)
>DroSec_CAF1 9650 108 + 1
AU--AUCU-----GAGCGAUUAUU-----CUUCCACCGCUCUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCCAACCUUU
..--....-----(((((......-----.......)))))............((((((((((.(((.....)))........((((.....))))....)))))))))).......... ( -27.82)
>DroEre_CAF1 1275 109 + 1
AUAUAUCC-----GAACGAUUAUU-----CUUCCACCGCUCUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGA-AACCGCACACAAAGUGCCAAAGUGAUUUGGAGCCAACCUUU
........-----(((.((....)-----)))).....................(((((((((.(((.....)))...-....((((.....))))....)))))))))........... ( -18.50)
>DroAna_CAF1 9343 120 + 1
UUAUAUAUACCAUAUACGAUUAUUUUCGGCUGCUGCCGCUCUUCCGACAUAAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCUAACCUUU
..........................((((....))))...........((..((((((((((.(((.....)))........((((.....))))....))))))))))..))...... ( -27.70)
>DroPer_CAF1 9449 86 + 1
----------------------------------ACAGAAAUGUCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGAGGCUAACCUUU
----------------------------------(((....))).....(((.((((((((((.(((.....)))........((((.....))))....)))))))).)).)))..... ( -18.80)
>consensus
AU__AUCU_____GA_CGAUUAUU_____CUUCCACCGCUCUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCCAACCUUU
.....................................................((((((((((.(((.....)))........((((.....))))....)))))))))).......... (-17.97 = -18.47 +   0.50) 

alignment

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secondary structure

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Window 2

Location 2,718,086 – 2,718,196
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -29.70
Consensus MFE -22.52
Energy contribution -22.47
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.98
Structure conservation index 0.76
SVM decision value 1.30
SVM RNA-class probability 0.939410
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2718086 110 - 20766785
AAAGGUUGGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGCUC-----AGAUAUAU
....((((((((.(((((((....((((.....))))(..((....))..)......)))))))))))))))(((....(((((((.....-----....)))))))-----.))).... ( -33.50)
>DroPse_CAF1 9326 86 - 1
AAAGGUUAGCCUCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGACAUUUCUGU----------------------------------
....(((((((.((((((((....((((.....))))(..((....))..)......)))))))))))))))..............---------------------------------- ( -23.70)
>DroSec_CAF1 9650 108 - 1
AAAGGUUGGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGCUC-----AGAU--AU
....((((((((.(((((((....((((.....))))(..((....))..)......)))))))))))))))(((....(((((((.....-----....)))))))-----.)))--.. ( -33.50)
>DroEre_CAF1 1275 109 - 1
AAAGGUUGGCUCCAAAUCACUUUGGCACUUUGUGUGCGGUU-UCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG-----AAUAAUCGUUC-----GGAUAUAU
....((((((.(((((((((....((((.....))))(..(-.....)..)......)))))))))))))))(((....(((((((.....-----....)))))))-----.))).... ( -30.40)
>DroAna_CAF1 9343 120 - 1
AAAGGUUAGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUUAUGUCGGAAGAGCGGCAGCAGCCGAAAAUAAUCGUAUAUGGUAUAUAUAA
...(((((((((((((((((....((((.....))))(..((....))..)......))))))))))......((....))))(((....))).....)))))((((((...)))))).. ( -33.40)
>DroPer_CAF1 9449 86 - 1
AAAGGUUAGCCUCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGACAUUUCUGU----------------------------------
....(((((((.((((((((....((((.....))))(..((....))..)......)))))))))))))))..............---------------------------------- ( -23.70)
>consensus
AAAGGUUAGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAGAGCGGUGGAAG_____AAUAAUCG_UC_____AGAU__AU
....(((((((.((((((((....((((.....))))(..((....))..)......)))))))))))))))................................................ (-22.52 = -22.47 +  -0.06) 

alignment

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secondary structure

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Window 3

Location 2,718,116 – 2,718,232
Length 116
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 79.61
Mean single sequence MFE -28.58
Consensus MFE -17.10
Energy contribution -17.77
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.60
SVM decision value 1.00
SVM RNA-class probability 0.898535
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2718116 116 + 20766785
CUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCCAACCUUUU-GGG-CAUUGCGCUCGGAGAUUGGGGGCCGCAGAUCC
..(((........((((((((((.(((.....)))........((((.....))))....)))))))))).((((..((((-(((-(.....)))))))).))))))).......... ( -35.00)
>DroPse_CAF1 9332 91 + 1
AUGUCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGAGGCUAACCUUUU-AAGCCAUUGU--------------------------
...............((((((((.(((.....)))........((((.....))))....)))))))).((((........-.)))).....-------------------------- ( -19.40)
>DroEre_CAF1 1305 115 + 1
CUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGA-AACCGCACACAAAGUGCCAAAGUGAUUUGGAGCCAACCUUUU-GGG-CAUUGUGCCGGGAGAUUGGGGGCCGCAGAUCC
..(((.........(((((((((.(((.....)))...-....((((.....))))....)))))))))..((((.(((((-((.-.......))))))).))))))).......... ( -31.60)
>DroYak_CAF1 9961 116 + 1
CUUCCGACAUUAACCCAAAUCACACAAAUGACUUCAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCCAACCUUUU-GGG-CAUUGUGCCCGUAGAUUGGGGGUCGCAGAUCC
....((((.....((((((((((.....((....)).......((((.....))))....)))))))))).((((.((..(-(((-(.....))))).)).))))..))))....... ( -39.80)
>DroAna_CAF1 9383 94 + 1
CUUCCGACAUAAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCUAACCUUUUUGGC-CAUUGUUCC-----------------------
.....((((.....(((((((((.(((.....)))........((((.....))))....)))))))))((((((.....)))))-)..))))..----------------------- ( -26.30)
>DroPer_CAF1 9455 91 + 1
AUGUCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGAGGCUAACCUUUU-AAGCCAUUGU--------------------------
...............((((((((.(((.....)))........((((.....))))....)))))))).((((........-.)))).....-------------------------- ( -19.40)
>consensus
CUUCCGACAUUAACCCAAAUCACACAAAUGACUUGAGAAAACCGCACACAAAGUGCCAAAGUGAUUUGGGGCCAACCUUUU_GGG_CAUUGUGCC_______________________
.............((((((((((.(((.....)))........((((.....))))....))))))))))................................................ (-17.10 = -17.77 +   0.67) 

alignment

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secondary structure

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Window 4

Location 2,718,116 – 2,718,232
Length 116
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 79.61
Mean single sequence MFE -30.54
Consensus MFE -22.64
Energy contribution -21.92
Covariance contribution -0.72
Combinations/Pair 1.16
Mean z-score -1.22
Structure conservation index 0.74
SVM decision value 0.27
SVM RNA-class probability 0.662316
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2718116 116 - 20766785
GGAUCUGCGGCCCCCAAUCUCCGAGCGCAAUG-CCC-AAAAGGUUGGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAG
.(((.((.(....))))))((((((((((.((-((.-.((((.(((....)))....)))))))).....))))).(((..((((((((((....))))))))))..))).))))).. ( -34.70)
>DroPse_CAF1 9332 91 - 1
--------------------------ACAAUGGCUU-AAAAGGUUAGCCUCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGACAU
--------------------------....((((..-.....(((((((.((((((((....((((.....))))(..((....))..)......))))))))))))))))))).... ( -24.01)
>DroEre_CAF1 1305 115 - 1
GGAUCUGCGGCCCCCAAUCUCCCGGCACAAUG-CCC-AAAAGGUUGGCUCCAAAUCACUUUGGCACUUUGUGUGCGGUU-UCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAG
...(((((((((.(((((((...(((.....)-)).-...)))))))...............((((.....))))))))-.((((((((((....)))))))))).....).)))).. ( -33.60)
>DroYak_CAF1 9961 116 - 1
GGAUCUGCGACCCCCAAUCUACGGGCACAAUG-CCC-AAAAGGUUGGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUGAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAG
.......((((..(((((((..((((.....)-)))-...))))))).((((((((((....((((.....))))(..((....))..)......)))))))))).....)))).... ( -41.40)
>DroAna_CAF1 9383 94 - 1
-----------------------GGAACAAUG-GCCAAAAAGGUUAGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUUAUGUCGGAAG
-----------------------.((.((.((-(((.....)))))..((((((((((....((((.....))))(..((....))..)......))))))))))....))))..... ( -25.50)
>DroPer_CAF1 9455 91 - 1
--------------------------ACAAUGGCUU-AAAAGGUUAGCCUCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGACAU
--------------------------....((((..-.....(((((((.((((((((....((((.....))))(..((....))..)......))))))))))))))))))).... ( -24.01)
>consensus
_______________________GGCACAAUG_CCC_AAAAGGUUAGCCCCAAAUCACUUUGGCACUUUGUGUGCGGUUUUCUCAAGUCAUUUGUGUGAUUUGGGUUAAUGUCGGAAG
..................................((....(.(((((((.((((((((....((((.....))))(..((....))..)......))))))))))))))).).))... (-22.64 = -21.92 +  -0.72) 

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:10 2006