Locus 3910

Sequence ID 2L_DroMel_CAF1
Location 11,421,282 – 11,421,444
Length 162
Max. P 0.975830
window6164 window6165 window6166

overview

Window 4

Location 11,421,282 – 11,421,379
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.49
Mean single sequence MFE -21.55
Consensus MFE -9.32
Energy contribution -9.52
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -3.62
Structure conservation index 0.43
SVM decision value 1.76
SVM RNA-class probability 0.975830
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11421282 97 + 22407834
--------CAUUC--ACAAUUCCAUU---CUCAGCUG--CUGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUC--UGAUUUGCAACA-GCAUAAGCC-----
--------.....--...........---....((((--.((((((((......(((((.....(((((......)))))...)))))...--.)))))))).))-)).......----- ( -23.70)
>DroPse_CAF1 168783 114 + 1
CACUCCAACACUCGAGCAACUCCAUU---GAUGGCUG--UUGAAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUCUGAUUUGCAACA-ACAAAAGCCCGAAA
...........(((.((....(((..---..))).((--(((.(((((......(((((.....(((((......)))))...)))))......))))).)))))-......)).))).. ( -21.30)
>DroEre_CAF1 146509 100 + 1
--------CAUUC--AGAAAUCCAUUCAACUCAGCUG--CUGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCGCGC--UGAUUUGCAACA-GCAUAAGCC-----
--------.....--..................((((--.((((((((......(((((.....(((((......)))))...)))))...--.)))))))).))-)).......----- ( -23.00)
>DroYak_CAF1 143591 97 + 1
--------CGUUC--ACAGCUCCGUU---CUCAGCUG--CUGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUC--UGAUUUGCAAGA-GCAUAAGCC-----
--------.((((--.(((((.....---...)))))--.((((((((......(((((.....(((((......)))))...)))))...--.)))))))).))-)).......----- ( -25.60)
>DroAna_CAF1 124268 100 + 1
--------CAUUU--ACAACUCCAUU---CUCAGCUGUGUUGAAAAUCUCUUUAUGACACAUUUUGAUAUUUAUUUAUUAUCUUGUCACUC--UGAUUUAAAAAACACCCAAGCC-----
--------.....--...........---....((((((((..(((((......(((((.....(((((......)))))...)))))...--.)))))....)))))...))).----- ( -13.90)
>DroPer_CAF1 168108 114 + 1
CACUCCAACACUCGAGCAACUCCAUU---GAUGGCUG--UUGAAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUUUGAUUGGCAACA-ACAAAAGCCCGAAA
...........(((.((....(((..---..))).((--(((..((((......(((((.....(((((......)))))...)))))......))))..)))))-......)).))).. ( -21.80)
>consensus
________CAUUC__ACAACUCCAUU___CUCAGCUG__CUGAAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUC__UGAUUUGCAACA_ACAUAAGCC_____
.................................(((....((.(((((......(((((.....(((((......)))))...)))))......))))).)).........)))...... ( -9.32 =  -9.52 +   0.20)

alignment

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secondary structure

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Window 5

Location 11,421,307 – 11,421,408
Length 101
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 87.07
Mean single sequence MFE -14.49
Consensus MFE -12.82
Energy contribution -13.18
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -2.10
Structure conservation index 0.88
SVM decision value 1.24
SVM RNA-class probability 0.934274
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11421307 101 + 22407834
UGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUGAUUUGCAACA-GCAUAAGCCACCCUGUUCUUUUUUCCCAUUUUUUUGUG
.(((((((......(((((.....(((((......)))))...)))))....)))))))((((-(...........)))))..................... ( -16.20)
>DroSec_CAF1 138909 100 + 1
UGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUGAUUUGGAACA-GCAUAAGCCACCCCGUUUUUU-UUUCCAUUUUUUUGUG
.(((((........(((((.....(((((......)))))...)))))....((..(((((..-....((((......))))...-.)))))..))))))). ( -13.20)
>DroSim_CAF1 145699 98 + 1
UGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUGAUUUGCAACA-GCAUAAGCCACCCCGUUUU---UUUCCAUUUUUUUGUG
((((((((......(((((.....(((((......)))))...)))))....))))))))...-((....))...........---................ ( -15.90)
>DroEre_CAF1 146537 96 + 1
UGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCGCGCUGAUUUGCAACA-GCAUAAGCCACCCUGUUU----UUCCCAUUUUUUAG-A
.(((((((......(((((.....(((((......)))))...)))))....)))))))((((-(...........))))).----..............-. ( -15.50)
>DroYak_CAF1 143616 96 + 1
UGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUGAUUUGCAAGA-GCAUAAGCCACCCCGAUU----UUUCCAUUUUUUAG-A
((((((((......(((((.....(((((......)))))...)))))....)))))))).(.-((....))).........----..............-. ( -16.30)
>DroAna_CAF1 124295 100 + 1
UGAAAAUCUCUUUAUGACACAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUGAUUUAAAAAACACCCAAGCCACCCCCAUUUUC-AGGACAUUUCAUUC-A
(((((.........(((((.....(((((......)))))...))))).(((((.............................))-)))...)))))...-. (  -9.85)
>consensus
UGCAAAUCUCCUUAUGACAUAUUUUGAUAUUUAUUUAUUAUCUUGUCACUCUGAUUUGCAACA_GCAUAAGCCACCCCGUUUU___UUUCCAUUUUUUUG_A
((((((((......(((((.....(((((......)))))...)))))....)))))))).......................................... (-12.82 = -13.18 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,421,347 – 11,421,444
Length 97
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 80.21
Mean single sequence MFE -25.17
Consensus MFE -16.63
Energy contribution -17.57
Covariance contribution 0.95
Combinations/Pair 1.29
Mean z-score -1.61
Structure conservation index 0.66
SVM decision value 0.38
SVM RNA-class probability 0.712638
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11421347 97 - 22407834
GACAAGUGAGUGCCGCCCCAGGAUGCGAAGCCCUACCACAAAAAAAUGGGAAAAAAGAACAGGGUGGCUUAUGC-UGUUGCAAAUCAGAGUGACAAGA
....((((...(((((((.(((.........))).(((........)))............)))))))...)))-)((..(........)..)).... ( -22.80)
>DroSec_CAF1 138949 96 - 1
GACAAGUGAGUGCCGCCCCAGGAUGCUAACUCCUACCACAAAAAAAUGGAAA-AAAAAACGGGGUGGCUUAUGC-UGUUCCAAAUCAGAGUGACAAGA
...........((((((((((((.......)))).(((........)))...-.......))))))))((((.(-((........))).))))..... ( -26.10)
>DroSim_CAF1 145739 94 - 1
GACAAGUGAGUGCCGCCCCAGGAUGCUAACUCCUACCACAAAAAAAUGGAAA---AAAACGGGGUGGCUUAUGC-UGUUGCAAAUCAGAGUGACAAGA
....((((...((((((((((((.......)))).(((........)))...---.....))))))))...)))-)((..(........)..)).... ( -28.60)
>DroEre_CAF1 146577 92 - 1
GACAAGUGAAUGCCGCCCCAGGAUGCGAAGUCCUAGU-CUAAAAAAUGGGAA----AAACAGGGUGGCUUAUGC-UGUUGCAAAUCAGCGCGACAAGA
....((((...(((((((.(((((.....)))))..(-((........))).----.....)))))))...)))-)(((((........))))).... ( -27.20)
>DroYak_CAF1 143656 92 - 1
GACAAGUGAGUGCCGCCCCAGGAUGCGAAUCCCUGCU-CUAAAAAAUGGAAA----AAUCGGGGUGGCUUAUGC-UCUUGCAAAUCAGAGUGACAAGA
..((..(((..((((((((.((((....))))....(-(((.....))))..----....))))))))...(((-....)))..)))...))...... ( -27.40)
>DroAna_CAF1 124335 86 - 1
GACAAGUGAGCGCCGCUCCU----------UCCUUCU-GAAUGAAAUGUCCU-GAAAAUGGGGGUGGCUUGGGUGUUUUUUAAAUCAGAGUGACAAGA
...........(((((((((----------...(((.-((........))..-)))...))))))))).....((((.(((......))).))))... ( -18.90)
>consensus
GACAAGUGAGUGCCGCCCCAGGAUGCGAACUCCUACC_CAAAAAAAUGGAAA___AAAACGGGGUGGCUUAUGC_UGUUGCAAAUCAGAGUGACAAGA
...........((((((((...........(((..............)))..........)))))))).......((((((........))))))... (-16.63 = -17.57 +   0.95)

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 11:04:33 2006