Locus 5332

Sequence ID 2R_DroMel_CAF1
Location 17,266,491 – 17,266,635
Length 144
Max. P 0.887863
window8516 window8517 window8518

overview

Window 6

Location 17,266,491 – 17,266,595
Length 104
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 73.16
Mean single sequence MFE -25.63
Consensus MFE -6.22
Energy contribution -6.98
Covariance contribution 0.76
Combinations/Pair 1.20
Mean z-score -1.78
Structure conservation index 0.24
SVM decision value 0.53
SVM RNA-class probability 0.771540
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17266491 104 + 20766785
UUU-UUUACGAUGCCCA-ACGC-UGGCCAUAAC---UUUUUCUCU-UUUUUUUUUAGCCAGCUACAAAAGCUGAAGGG------AGUGA--AAAAAAAGUGUUGCAGUGGCAUAUAACU
...-......(((((((-((((-(.........---((((((.((-(((((.......(((((.....))))))))))------)).))--))))..)))))))....)))))...... ( -23.91)
>DroPse_CAF1 23399 105 + 1
UUUUUUUAUGAUCCCUAGGCGCUUGGCCAUAAU---UUUGUUCCUUUUUUUCUGCUG----------UGGCAGAAGGGGCACUCACAAAA-AAAAAAUGUUUAACAGUGGCAUAUAACU
(((((((.(((......(((.....))).....---..(((((((.....(((((..----------..)))))))))))).))).))))-)))..(((((.......)))))...... ( -23.70)
>DroSec_CAF1 1562 105 + 1
UUUUUUUACGAUGCCCA-ACAC-UGUCCAUAAC---UUUUUUUCGCUUUUUUUUUAGCUAGCUACAAAAGCUGAAGGG------AGUGA--AAA-AAAGUGUUGCAGUGGCAUAUAACU
..........(((((..-..((-(((.....((---(((((((((((((..((((((((.........))))))))))------)))))--)))-)))))...))))))))))...... ( -33.30)
>DroEre_CAF1 1786 107 + 1
UUU-UUUACGAUGCCAA-ACGC-UGGCCAUAAUGUGUUUUUCCCU-UUUUGUUUUAGCCAGCUACAAAAGCAGCAGGG------AGUGA--AAAAAAUGUGUUGCAGUGGCAUAUAACU
...-......((((((.-..((-((((...((((...........-...))))...)))))).......((((((.(.------..(..--..)...).))))))..))))))...... ( -27.64)
>DroPer_CAF1 23590 105 + 1
UUU-UUUAUGAUCCCCAGGCGCUUGGCCAUAAU---UUUGUUCUUUUUUUUUUUUUG----------UGGCAGAAGGGGCACUCAAAAAAAAAAAAAUGUUUAACAGUGGCAUAUAACU
...-.(((((.....(((....)))(((((...---.(((..(((((((((((((((----------.(((.......)).).)))))))))))))).)..)))..))))).))))).. ( -19.60)
>consensus
UUU_UUUACGAUGCCCA_ACGC_UGGCCAUAAU___UUUUUUCCU_UUUUUUUUUAGC_AGCUACAAAAGCAGAAGGG______AGUGA__AAAAAAUGUGUUGCAGUGGCAUAUAACU
.........................(((((...................(((((((((...........)))))))))....................(.....).)))))........ ( -6.22 =  -6.98 +   0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,266,491 – 17,266,595
Length 104
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 73.16
Mean single sequence MFE -23.16
Consensus MFE -4.06
Energy contribution -4.38
Covariance contribution 0.32
Combinations/Pair 1.35
Mean z-score -1.87
Structure conservation index 0.18
SVM decision value 0.95
SVM RNA-class probability 0.887863
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17266491 104 - 20766785
AGUUAUAUGCCACUGCAACACUUUUUUU--UCACU------CCCUUCAGCUUUUGUAGCUGGCUAAAAAAAAA-AGAGAAAAA---GUUAUGGCCA-GCGU-UGGGCAUCGUAAA-AAA
..(((((((((....((((.........--.....------.......((....)).((((((((........-.........---....))))))-))))-))))))).)))).-... ( -21.90)
>DroPse_CAF1 23399 105 - 1
AGUUAUAUGCCACUGUUAAACAUUUUUU-UUUUGUGAGUGCCCCUUCUGCCA----------CAGCAGAAAAAAAGGAACAAA---AUUAUGGCCAAGCGCCUAGGGAUCAUAAAAAAA
.........................(((-((((((((...(((.((((((..----------..)))))).............---.....(((.....)))..))).))))))))))) ( -23.70)
>DroSec_CAF1 1562 105 - 1
AGUUAUAUGCCACUGCAACACUUU-UUU--UCACU------CCCUUCAGCUUUUGUAGCUAGCUAAAAAAAAAGCGAAAAAAA---GUUAUGGACA-GUGU-UGGGCAUCGUAAAAAAA
..((((((((((((((...(((((-(((--((...------......((((.....)))).(((........)))))))))))---))....).))-))..-..))))).))))..... ( -25.90)
>DroEre_CAF1 1786 107 - 1
AGUUAUAUGCCACUGCAACACAUUUUUU--UCACU------CCCUGCUGCUUUUGUAGCUGGCUAAAACAAAA-AGGGAAAAACACAUUAUGGCCA-GCGU-UUGGCAUCGUAAA-AAA
..((((((((((.(((....(((.....--....(------(((((((((....)))))((.......))...-)))))..........)))....-))).-.)))))).)))).-... ( -24.61)
>DroPer_CAF1 23590 105 - 1
AGUUAUAUGCCACUGUUAAACAUUUUUUUUUUUUUGAGUGCCCCUUCUGCCA----------CAAAAAAAAAAAAAGAACAAA---AUUAUGGCCAAGCGCCUGGGGAUCAUAAA-AAA
..((((((.((..((((.....((((((((((((((.(.((.......))).----------)))))))))))))).))))..---.....(((.....)))..)).)).)))).-... ( -19.70)
>consensus
AGUUAUAUGCCACUGCAACACAUUUUUU__UCACU______CCCUUCUGCUUUUGUAGCU_GCUAAAAAAAAA_AGGAAAAAA___AUUAUGGCCA_GCGU_UGGGCAUCGUAAA_AAA
..(((((((((...((...............................((((.........))))............................((...))))...))))).))))..... ( -4.06 =  -4.38 +   0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,266,524 – 17,266,635
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.57
Mean single sequence MFE -20.46
Consensus MFE -9.67
Energy contribution -9.63
Covariance contribution -0.04
Combinations/Pair 1.10
Mean z-score -2.07
Structure conservation index 0.47
SVM decision value 0.51
SVM RNA-class probability 0.763924
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17266524 111 - 20766785
UCGCUGGCAAUUGCAUUCAUCCUUCAACAAAUUAAAACAAAGUUAUAUGCCACUGCAACACUUUUUUU--UCACU------CCCUUCAGCUUUUGUAGCUGGCUAAAAAAAAA-AGAGAA
..(((((((...((...........................))....)))))..))....((((((((--(....------....((((((.....))))))......)))))-)))).. ( -17.27)
>DroPse_CAF1 23435 109 - 1
UCAGUGGCAAUUGCACUCAUCCUUCAACAAAUUAAAACAAAGUUAUAUGCCACUGUUAAACAUUUUUU-UUUUGUGAGUGCCCCUUCUGCCA----------CAGCAGAAAAAAAGGAAC
.((((((((...((...........................))....)))))))).......((((((-((((((..(((.(......).))----------).)))))))))))).... ( -21.63)
>DroSec_CAF1 1596 111 - 1
UCGGUGGCAAUUGCAUUCAUCCUUCAACAAAUUAAAACAAAGUUAUAUGCCACUGCAACACUUU-UUU--UCACU------CCCUUCAGCUUUUGUAGCUAGCUAAAAAAAAAGCGAAAA
.((((((((...((...........................))....)))))))).........-...--.....------...(((.((((((.(((....)))....))))))))).. ( -18.33)
>DroEre_CAF1 1822 111 - 1
UCGGUGGCAAUUGCAUUCAUCCUUCAACAAAUUAAAACAAAGUUAUAUGCCACUGCAACACAUUUUUU--UCACU------CCCUGCUGCUUUUGUAGCUGGCUAAAACAAAA-AGGGAA
.((((((((...((...........................))....)))))))).............--....(------(((((((((....)))))((.......))...-))))). ( -23.13)
>DroPer_CAF1 23625 110 - 1
UCAGUGGCAAUUGCACUCAUCCUUCAACAAAUUAAAACAAAGUUAUAUGCCACUGUUAAACAUUUUUUUUUUUUUGAGUGCCCCUUCUGCCA----------CAAAAAAAAAAAAAGAAC
.((((((((...((...........................))....)))))))).......((((((((((((((.(.((.......))).----------)))))))))))))).... ( -21.93)
>consensus
UCGGUGGCAAUUGCAUUCAUCCUUCAACAAAUUAAAACAAAGUUAUAUGCCACUGCAACACAUUUUUU__UCACU______CCCUUCUGCUUUUGUAGCU_GCUAAAAAAAAA_AGGAAA
.((((((((...((...........................))....))))))))................................................................. ( -9.67 =  -9.63 +  -0.04)

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 11:42:19 2006