Locus 4570

Sequence ID 2L_DroMel_CAF1
Location 13,113,257 – 13,113,394
Length 137
Max. P 0.726492
window7199 window7200 window7201

overview

Window 9

Location 13,113,257 – 13,113,363
Length 106
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 83.12
Mean single sequence MFE -19.59
Consensus MFE -14.64
Energy contribution -14.96
Covariance contribution 0.32
Combinations/Pair 1.27
Mean z-score -1.61
Structure conservation index 0.75
SVM decision value 0.14
SVM RNA-class probability 0.603127
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13113257 106 - 22407834
AAUUUCUUUUUAUCUUAAGGACAAAAUCUUCCUUAACAGUUCUCUUAAAAGAAAACUACCCUGAU------ACUCUUACACGCUUAACAGGCCAUGUUACAACUGGGACCAA
..............(((((((........))))))).((((.(((....))).)))).(((....------......(((.(((.....)))..))).......)))..... ( -14.93)
>DroSec_CAF1 6330 104 - 1
AAU--CUAUUUAUCUUAAGGACAAAAUCAUCCUUAACAGUUCUCUUAAGAGAGAACUACCCUGGU------ACUCUUGCAUCCCUAACAGGCCCUGUUAAAACUGGGACCAA
...--.....(((((((((((........))))))).((((((((....)))))))).....)))------).................(((((.((....)).))).)).. ( -24.00)
>DroSim_CAF1 6444 104 - 1
AAU--CUCUUUAUCUGAAGGACAAAAUCUUCCUUAACAGUUCUCUUAAGGGAGAACUACCCUGGU------ACUCUUACACCCCUAACAGGACCUGUUAAAACUGGGACCAA
...--...........(((((........)))))...((((((((....)))))))).(((.(((------........)))..((((((...)))))).....)))..... ( -22.70)
>DroEre_CAF1 8350 109 - 1
AAU--CUCUUUAUCUCAAACACAAUACCUUCUCUGGCAGUUCUCUUAAGGGAUAACUACCCUAGUGCUCUUACUCUUACGUCCUUAACAGGCCAUGUUAAAAC-GGGACCAA
...--.....................((......))..((.....((((((...((((...)))).)))))).....))((((((((((.....)))))....-)))))... ( -16.30)
>DroYak_CAF1 6560 104 - 1
AAU--CUCUUUAUCUUAGGGACAAUAUAUUCGUUGACAGUUCUCUUAAGGGAGAACUACCCCAGU------ACUCUUACACCCUUCACAGGCCAUGUUAAAACCGGGUCCAA
...--...........((((.((((......))))..((((((((....))))))))........------.........)))).....((((..((....))..))))... ( -20.00)
>consensus
AAU__CUCUUUAUCUUAAGGACAAAAUCUUCCUUAACAGUUCUCUUAAGGGAGAACUACCCUGGU______ACUCUUACACCCUUAACAGGCCAUGUUAAAACUGGGACCAA
..............(((((((........))))))).((((((((....)))))))).(((.(((......)))..........(((((.....))))).....)))..... (-14.64 = -14.96 +   0.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,113,292 – 13,113,394
Length 102
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -21.84
Consensus MFE -15.48
Energy contribution -15.40
Covariance contribution -0.08
Combinations/Pair 1.30
Mean z-score -1.82
Structure conservation index 0.71
SVM decision value 0.41
SVM RNA-class probability 0.726492
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13113292 102 + 22407834
AAGAGU------AUCAGGGUAGUUUUCUUUUAAGAGAACUGUUAAGGAAGAUUUUGUCCUUAAGAUAAAAAGAAAUUUAAAAGUAUUCAUUGAAUUUAGGCUUAACAU
..((((------(((....(((((((((....)))))))))(((((((........))))))))))......((((((((.........))))))))..))))..... ( -18.80)
>DroSec_CAF1 6365 100 + 1
AAGAGU------ACCAGGGUAGUUCUCUCUUAAGAGAACUGUUAAGGAUGAUUUUGUCCUUAAGAUAAAUAG--AUUUAAAAGAAUUCAUUGAAUUUAGGCUUAACAU
..((((------.......(((((((((....)))))))))((((((((......))))))))......(((--((((((.........))))))))).))))..... ( -23.10)
>DroSim_CAF1 6479 100 + 1
AAGAGU------ACCAGGGUAGUUCUCCCUUAAGAGAACUGUUAAGGAAGAUUUUGUCCUUCAGAUAAAGAG--AUUAAAAAGAAAACAUUGAAUUUAGGCUCAACAU
..((((------.((..((((((((((......))))))))))..))....(((((((.....)))))))..--.........................))))..... ( -19.90)
>DroEre_CAF1 8384 106 + 1
AAGAGUAAGAGCACUAGGGUAGUUAUCCCUUAAGAGAACUGCCAGAGAAGGUAUUGUGUUUGAGAUAAAGAG--AUUAAAAAGAAUUCAUUGAAUUCGGGCUCAAUAU
.............((..(((((((.((......)).)))))))..))...((((((.(((((((...((..(--(((......))))..))...))))))).)))))) ( -22.90)
>DroYak_CAF1 6595 100 + 1
AAGAGU------ACUGGGGUAGUUCUCCCUUAAGAGAACUGUCAACGAAUAUAUUGUCCCUAAGAUAAAGAG--AUUAAAAAGAAGUCAUUGAGCUCAGGCUCAACAU
..((((------.(((((.((((((((......))))))))((((........(((((.....)))))...(--(((.......)))).)))).)))))))))..... ( -24.50)
>consensus
AAGAGU______ACCAGGGUAGUUCUCCCUUAAGAGAACUGUUAAGGAAGAUUUUGUCCUUAAGAUAAAGAG__AUUAAAAAGAAUUCAUUGAAUUUAGGCUCAACAU
..((((.......((..((((((((((......))))))))))..))....(((((((.....))))))).............................))))..... (-15.48 = -15.40 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,113,292 – 13,113,394
Length 102
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 82.85
Mean single sequence MFE -17.04
Consensus MFE -11.66
Energy contribution -11.90
Covariance contribution 0.24
Combinations/Pair 1.36
Mean z-score -1.79
Structure conservation index 0.68
SVM decision value 0.28
SVM RNA-class probability 0.667455
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13113292 102 - 22407834
AUGUUAAGCCUAAAUUCAAUGAAUACUUUUAAAUUUCUUUUUAUCUUAAGGACAAAAUCUUCCUUAACAGUUCUCUUAAAAGAAAACUACCCUGAU------ACUCUU
.........................................(((((((((((........))))))).((((.(((....))).)))).....)))------)..... ( -10.40)
>DroSec_CAF1 6365 100 - 1
AUGUUAAGCCUAAAUUCAAUGAAUUCUUUUAAAU--CUAUUUAUCUUAAGGACAAAAUCAUCCUUAACAGUUCUCUUAAGAGAGAACUACCCUGGU------ACUCUU
.......(((........................--.........(((((((........))))))).((((((((....)))))))).....)))------...... ( -18.00)
>DroSim_CAF1 6479 100 - 1
AUGUUGAGCCUAAAUUCAAUGUUUUCUUUUUAAU--CUCUUUAUCUGAAGGACAAAAUCUUCCUUAACAGUUCUCUUAAGGGAGAACUACCCUGGU------ACUCUU
((((((((......))))))))............--.....((((..(((((........)))))...((((((((....)))))))).....)))------)..... ( -17.40)
>DroEre_CAF1 8384 106 - 1
AUAUUGAGCCCGAAUUCAAUGAAUUCUUUUUAAU--CUCUUUAUCUCAAACACAAUACCUUCUCUGGCAGUUCUCUUAAGGGAUAACUACCCUAGUGCUCUUACUCUU
.....((((.(((((((...))))))........--.............................((.((((.(((....))).)))).))...).))))........ ( -15.40)
>DroYak_CAF1 6595 100 - 1
AUGUUGAGCCUGAGCUCAAUGACUUCUUUUUAAU--CUCUUUAUCUUAGGGACAAUAUAUUCGUUGACAGUUCUCUUAAGGGAGAACUACCCCAGU------ACUCUU
..(((((((....)))))))..............--............(((.((((......))))..((((((((....))))))))..)))...------...... ( -24.00)
>consensus
AUGUUGAGCCUAAAUUCAAUGAAUUCUUUUUAAU__CUCUUUAUCUUAAGGACAAAAUCUUCCUUAACAGUUCUCUUAAGGGAGAACUACCCUGGU______ACUCUU
.(((((((......)))))))........................(((((((........))))))).((((((((....)))))))).................... (-11.66 = -11.90 +   0.24)

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 11:21:17 2006