Locus 3195

Sequence ID X_DroMel_CAF1
Location 8,466,717 – 8,466,934
Length 217
Max. P 0.704721
window5241 window5242 window5243 window5244

overview

Window 1

Location 8,466,717 – 8,466,820
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.16
Mean single sequence MFE -29.05
Consensus MFE -21.20
Energy contribution -21.61
Covariance contribution 0.41
Combinations/Pair 1.22
Mean z-score -1.48
Structure conservation index 0.73
SVM decision value 0.36
SVM RNA-class probability 0.702765
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466717 103 + 22224390
---------U-CUUCAGCUGAAAAUGUCGUUGGCU------GCCAGUUAAAGUUGGUGACGAGGCGUGAG-AGGUCUUUGUCACUACUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAG
---------.-...........(((((((..((((------(.....((((((((((((((((((....)-....))))))))))).......)))))).....)))))..))))))).. ( -30.91)
>DroSec_CAF1 9456 101 + 1
---------U-UUUCAGCUGAAAAUGUCGUUGGUU------GCCAGUUAAAGUUGGUGACGAGGCGUG---AGGUCUUUGUCACUAGUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAG
---------.-...........(((((((..((((------(.....((((((((((((((((((...---.)..))))))))))).......)))))).....)))))..))))))).. ( -29.21)
>DroSim_CAF1 18283 101 + 1
---------U-UUUCAGCUAAAAAUGUCGUUGGUU------GCCAGUUAAAGUUGGUGACGAGGCGUG---AGGUCUUUGUCACUAGUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAG
---------.-.....(((((((..(((....((.------.((((......))))..))((((((..---((((......((....))....))))..))))))))))))))))..... ( -29.60)
>DroEre_CAF1 15675 99 + 1
AUUUUCCGAUUUUGCUGCCGAAUAUGUCGCUUGUU------GCCAGUUAAAGUUGGCGCCGAG--------------UUGCCACUACAGUUGUGCUUUGU-UUUCAGCUUUUGGCAUUAG
...............(((((((...((.(((((.(------(((((......)))))).))))--------------).))......(((((........-...)))))))))))).... ( -24.00)
>DroYak_CAF1 16233 120 + 1
AUUUCCCGAUUUUGCUGCUGAAAAUGCCGCUAGUUGGUUAUGCCGAUUAAAGUUGGUGACGAGGAGUGAGCAUGUUUUUGUCACUACUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAG
.....((((((..((.((.......)).)).))))))....(((((.((((((((((((((((((.........)))))))))))).......))))))....)))))............ ( -31.51)
>consensus
_________U_UUUCAGCUGAAAAUGUCGUUGGUU______GCCAGUUAAAGUUGGUGACGAGGCGUG___AGGUCUUUGUCACUACUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAG
................((((((...(((((((((.......))))).(((((((((((((((((...........))))))))))).......)))))).....)))).))))))..... (-21.20 = -21.61 +   0.41)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,466,780 – 8,466,899
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 92.72
Mean single sequence MFE -29.89
Consensus MFE -22.75
Energy contribution -22.12
Covariance contribution -0.62
Combinations/Pair 1.12
Mean z-score -1.79
Structure conservation index 0.76
SVM decision value -0.00
SVM RNA-class probability 0.531224
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466780 119 + 22224390
UCACUACUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAGCACUAUGGCUUCUUUCGUUACACUUGAUGCUUUUAUUUCGGCUGCAUUUUUGUAGCCAUUGCAGUUGCCACAGCAACUU
...........(((((..(((((...((.....))...)))))..((((..((..(((((....)))))..........(((((((....))))))).....))..)))).)))))... ( -29.30)
>DroSec_CAF1 9517 119 + 1
UCACUAGUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAGCACUAUGGCUUCUUUCGUUGCACUCGAUGCUUUUAUUGCGGCUGAAUUUUUGUAGCCGUUGCAGUUGCCACAGCAACUU
...(.(((((...(((..(((((...((.....))...)))))...)))..........))))).).(((.......(((((((........))))))).)))(((((....))))).. ( -30.62)
>DroSim_CAF1 18344 119 + 1
UCACUAGUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAGCACUAUGGCUUCUUUCGUUACACUCGAUGCUUUUAUUGCGGCUGAAUUUUUGUAGCCGUUGCAGUUGCCACAGCAACUU
...(.(((((...(((..(((((...((.....))...)))))...)))..........))))).).(((.......(((((((........))))))).)))(((((....))))).. ( -30.32)
>DroEre_CAF1 15735 118 + 1
CCACUACAGUUGUGCUUUGU-UUUCAGCUUUUGGCAUUAGCACUAUGGCUUCUUUCGUUACACUUGAUGCUUUCAUUCUGGCGGAAUUUUGGUAGCUGUUGCAGUUGCCACAGCAACUU
......((...(((((.(((-(..........))))..)))))..))(((..((((((((....(((.....)))...))))))))...(((((((((...))))))))).)))..... ( -29.30)
>consensus
UCACUACUGUUUUGCUUUGUGUUUCGGCUUUUGGCAUUAGCACUAUGGCUUCUUUCGUUACACUCGAUGCUUUUAUUGCGGCUGAAUUUUUGUAGCCGUUGCAGUUGCCACAGCAACUU
..........................(((..(((((...(((..((((((.(..(((.......))).(((........))).........).)))))))))...))))).)))..... (-22.75 = -22.12 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,466,780 – 8,466,899
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 92.72
Mean single sequence MFE -26.10
Consensus MFE -20.66
Energy contribution -20.72
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.91
Structure conservation index 0.79
SVM decision value 0.36
SVM RNA-class probability 0.704721
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466780 119 - 22224390
AAGUUGCUGUGGCAACUGCAAUGGCUACAAAAAUGCAGCCGAAAUAAAAGCAUCAAGUGUAACGAAAGAAGCCAUAGUGCUAAUGCCAAAAGCCGAAACACAAAGCAAAACAGUAGUGA
...(((((((((((...((((((((((((...((((.............))))....)))).(....)..)))))..)))...))))....((...........))...)))))))... ( -28.82)
>DroSec_CAF1 9517 119 - 1
AAGUUGCUGUGGCAACUGCAACGGCUACAAAAAUUCAGCCGCAAUAAAAGCAUCGAGUGCAACGAAAGAAGCCAUAGUGCUAAUGCCAAAAGCCGAAACACAAAGCAAAACACUAGUGA
...((((((((((...((((..((((..........))))((.......))......)))).(....)..))))).(((.....((.....)).....)))..)))))........... ( -26.00)
>DroSim_CAF1 18344 119 - 1
AAGUUGCUGUGGCAACUGCAACGGCUACAAAAAUUCAGCCGCAAUAAAAGCAUCGAGUGUAACGAAAGAAGCCAUAGUGCUAAUGCCAAAAGCCGAAACACAAAGCAAAACACUAGUGA
...((((((((((...((((..((((..........))))((.......))......)))).(....)..))))).(((.....((.....)).....)))..)))))........... ( -24.00)
>DroEre_CAF1 15735 118 - 1
AAGUUGCUGUGGCAACUGCAACAGCUACCAAAAUUCCGCCAGAAUGAAAGCAUCAAGUGUAACGAAAGAAGCCAUAGUGCUAAUGCCAAAAGCUGAAA-ACAAAGCACAACUGUAGUGG
..((.(((((.((....)).))))).)).......(((((((......(((((...(.((..(....)..)))...)))))..........(((....-....)))....)))..)))) ( -25.60)
>consensus
AAGUUGCUGUGGCAACUGCAACGGCUACAAAAAUUCAGCCGCAAUAAAAGCAUCAAGUGUAACGAAAGAAGCCAUAGUGCUAAUGCCAAAAGCCGAAACACAAAGCAAAACACUAGUGA
.....(((.(((((...(((..((((.......................((((...))))..(....).))))....)))...)))))..))).......................... (-20.66 = -20.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,466,820 – 8,466,934
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.93
Mean single sequence MFE -28.00
Consensus MFE -16.69
Energy contribution -16.81
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -2.06
Structure conservation index 0.60
SVM decision value 0.11
SVM RNA-class probability 0.587757
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466820 114 - 22224390
-----UAGUUUGCAAACGUUUGCGAACAACACCAUAGAUAAAGUUGCUGUGGCAACUGCA-AUGGCUACAAAAAUGCAGCCGAAAUAAAAGCAUCAAGUGUAACGAAAGAAGCCAUAGUG
-----..((((((((....))))))))..............((((((....))))))((.-(((((((((...((((.............))))....)))).(....)..))))).)). ( -30.22)
>DroSec_CAF1 9557 108 - 1
-----UAGUUCGCAAAUGUUUGCGA------CCAUAGAUAAAGUUGCUGUGGCAACUGCA-ACGGCUACAAAAAUUCAGCCGCAAUAAAAGCAUCGAGUGCAACGAAAGAAGCCAUAGUG
-----..(.((((((....))))))------.)............((((((((...((((-..((((..........))))((.......))......)))).(....)..)))))))). ( -30.90)
>DroSim_CAF1 18384 114 - 1
-----UAGUUGGCAAAUGUUUGCGAACAACACCAUAGAUAAAGUUGCUGUGGCAACUGCA-ACGGCUACAAAAAUUCAGCCGCAAUAAAAGCAUCGAGUGUAACGAAAGAAGCCAUAGUG
-----..(((.((((....)))).)))..................((((((((...((((-..((((..........))))((.......))......)))).(....)..)))))))). ( -29.30)
>DroEre_CAF1 15774 111 - 1
--------UUUGCAAAUGUUUACCAAGAACACCAUUGAAGAAGUUGCUGUGGCAACUGCA-ACAGCUACCAAAAUUCCGCCAGAAUGAAAGCAUCAAGUGUAACGAAAGAAGCCAUAGUG
--------........(((((.....)))))..............((((((((...((((-...(((......((((.....))))...)))......)))).(....)..)))))))). ( -20.00)
>DroYak_CAF1 16353 119 - 1
CAAACUAUUUGGCGAAUGUUUACGAAUAAUGGCAUUGAAAAAGUUGCUGUGGCAACUGCAAACAGCUCCAAAAAUGCAGCCACAAUAAAGGCAGCAAGUGUAACGAAAGAAGCCAUAG-G
....(((..((((......(((((.....(((..(((....((((((....)))))).....)))..)))....(((.(((........))).)))..)))))(....)..)))))))-. ( -29.60)
>consensus
_____UAGUUGGCAAAUGUUUGCGAACAACACCAUAGAUAAAGUUGCUGUGGCAACUGCA_ACGGCUACAAAAAUUCAGCCGCAAUAAAAGCAUCAAGUGUAACGAAAGAAGCCAUAGUG
...........((((....))))......................((((((((...((((....(((......................)))......)))).(....)..)))))))). (-16.69 = -16.81 +   0.12)

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 10:53:32 2006