Locus 3671

Sequence ID 2R_DroMel_CAF1
Location 12,214,750 – 12,214,841
Length 91
Max. P 0.736545
window5971 window5972

overview

Window 1

Location 12,214,750 – 12,214,841
Length 91
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 80.04
Mean single sequence MFE -16.43
Consensus MFE -12.45
Energy contribution -12.32
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.76
SVM decision value 0.44
SVM RNA-class probability 0.736545
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12214750 91 + 20766785
UC--------CUGUGCUAUCAGUGUUUU---UCUUCUUGCUGUGCAUUUUAUUAUUUUGUUAUUUGCAUUUGCAUGGAAAUAUGAA----UUCCCUGUUCUCAGCU
..--------....(((.........((---(((...(((.(((((....((......))....)))))..))).)))))...(((----(.....))))..))). ( -14.60)
>DroPse_CAF1 78018 96 + 1
CA--------CU--CCUACAGCUGCUACUCCCGUCCUUGCUGUGCAUUUUAUUAUUUUGUUAUUUGCAUUUGCAUGGAAAUAUGAAAUAUUCUCCUGUUCUCAGUC
.(--------((--...((((..(....((...(((.(((.(((((....((......))....)))))..))).))).....))......)..))))....))). ( -13.80)
>DroEre_CAF1 83740 99 + 1
UCCUGUAGUCCUGUGCUAUCAGUGUUUU---CCUCCUUGCUGUGCAUUUUAUUAUUUUGUUAUUUGCAUUUGCAUGGAAAUAUGAA----UUCCCUGUUCUCAGCU
..(((.((..(.......(((....(((---((....(((.(((((....((......))....)))))..))).)))))..))).----......)..))))).. ( -17.24)
>DroYak_CAF1 78825 91 + 1
UG--------CUGUGCUAUCAGUGUUUU---UCUCCAUGCUGUGCAUUUUAUUAUUUUGUUAUUUGCAUUUGCAUGGAAAUAUGAA----UUCCCUGUUCUCAGCU
.(--------(((.(....(((.((((.---..(((((((.(((((....((......))....)))))..))))))).....)))----)...)))..).)))). ( -23.80)
>DroAna_CAF1 70914 95 + 1
CC--------UUACCCCAUACGUGCUUU-UGUGUCCUUGCUGUGCAUUUUAUUAUUUCGUUAUUUGCAUUUGCAUGGAAAUAUGAAA--CUCUCCUGUUCUCAGCU
..--------.............((...-(((.(((.(((.(((((..................)))))..))).))).)))(((((--(......))).))))). ( -15.37)
>DroPer_CAF1 78669 96 + 1
CA--------CU--CCUACAGCUGCUACUCCCGUCCUUGCUGUGCAUUUUAUUAUUUUGUUAUUUGCAUUUGCAUGGAAAUAUGAAAUAUUCUCCUGUUCUCAGUC
.(--------((--...((((..(....((...(((.(((.(((((....((......))....)))))..))).))).....))......)..))))....))). ( -13.80)
>consensus
CC________CUGUCCUAUAAGUGCUUU___CCUCCUUGCUGUGCAUUUUAUUAUUUUGUUAUUUGCAUUUGCAUGGAAAUAUGAA____UCCCCUGUUCUCAGCU
.................................(((.(((.(((((....((......))....)))))..))).)))................(((....))).. (-12.45 = -12.32 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,214,750 – 12,214,841
Length 91
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 80.04
Mean single sequence MFE -16.83
Consensus MFE -10.02
Energy contribution -9.85
Covariance contribution -0.17
Combinations/Pair 1.17
Mean z-score -1.69
Structure conservation index 0.60
SVM decision value 0.12
SVM RNA-class probability 0.595332
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12214750 91 - 20766785
AGCUGAGAACAGGGAA----UUCAUAUUUCCAUGCAAAUGCAAAUAACAAAAUAAUAAAAUGCACAGCAAGAAGA---AAAACACUGAUAGCACAG--------GA
.((((......(((((----(....)))))).(((....)))......................)))).......---......(((......)))--------.. ( -15.70)
>DroPse_CAF1 78018 96 - 1
GACUGAGAACAGGAGAAUAUUUCAUAUUUCCAUGCAAAUGCAAAUAACAAAAUAAUAAAAUGCACAGCAAGGACGGGAGUAGCAGCUGUAGG--AG--------UG
..(((....)))...............((((.(((....))).....................(((((....((....))....))))).))--))--------.. ( -16.40)
>DroEre_CAF1 83740 99 - 1
AGCUGAGAACAGGGAA----UUCAUAUUUCCAUGCAAAUGCAAAUAACAAAAUAAUAAAAUGCACAGCAAGGAGG---AAAACACUGAUAGCACAGGACUACAGGA
.((((......(((((----(....)))))).(((....)))......................)))).......---......(((.((((....).)))))).. ( -17.20)
>DroYak_CAF1 78825 91 - 1
AGCUGAGAACAGGGAA----UUCAUAUUUCCAUGCAAAUGCAAAUAACAAAAUAAUAAAAUGCACAGCAUGGAGA---AAAACACUGAUAGCACAG--------CA
.((((.(..(((.(..----..)...(((((((((...((((..................))))..)))))))))---......)))....).)))--------). ( -21.47)
>DroAna_CAF1 70914 95 - 1
AGCUGAGAACAGGAGAG--UUUCAUAUUUCCAUGCAAAUGCAAAUAACGAAAUAAUAAAAUGCACAGCAAGGACACA-AAAGCACGUAUGGGGUAA--------GG
.((((......(((((.--.......))))).(((....)))......................)))).........-..................--------.. ( -13.80)
>DroPer_CAF1 78669 96 - 1
GACUGAGAACAGGAGAAUAUUUCAUAUUUCCAUGCAAAUGCAAAUAACAAAAUAAUAAAAUGCACAGCAAGGACGGGAGUAGCAGCUGUAGG--AG--------UG
..(((....)))...............((((.(((....))).....................(((((....((....))....))))).))--))--------.. ( -16.40)
>consensus
AGCUGAGAACAGGAAA____UUCAUAUUUCCAUGCAAAUGCAAAUAACAAAAUAAUAAAAUGCACAGCAAGGACA___AAAACACUGAUAGCACAG________GA
.((((......(((((..........))))).(((....)))......................))))...................................... (-10.02 =  -9.85 +  -0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:27 2006