Locus 3800

Sequence ID 2L_DroMel_CAF1
Location 11,104,838 – 11,105,004
Length 166
Max. P 0.997164
window5993 window5994 window5995

overview

Window 3

Location 11,104,838 – 11,104,931
Length 93
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 74.59
Mean single sequence MFE -41.15
Consensus MFE -25.76
Energy contribution -24.77
Covariance contribution -1.00
Combinations/Pair 1.33
Mean z-score -3.27
Structure conservation index 0.63
SVM decision value 2.81
SVM RNA-class probability 0.997164
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11104838 93 + 22407834
GUCCUCAUCGUCAUCAUUUAGGUGCAGGAGAUCAGCCUCAGGUGGCUCCUGAGGCAGC---GCCGCCGAUGACGAGGAUGUCACCCCCUGUCCACU
.......((((((((.....(((((..(....).((((((((.....)))))))).))---)))...))))))))(((((........)))))... ( -39.40)
>DroPse_CAF1 8983 87 + 1
GUCCUCGUCGUCGUCGUUCAAAUGCAGGAGAUCAGCCUCGGGGGGCUCUUGAGGUAAC---GACGACGACGAGGAGGAGGUCACUCC------ACC
.((((((((((((((((((.....(((((.....((((....)))))))))..).)))---))))))))))))))((((....))))------... ( -48.40)
>DroGri_CAF1 9045 88 + 1
AUCCUCGUCGUCGUCAUUCAAAUGCAGGAGAUCAGCCUCGGGCGGCUCUUGAGGUAUGUGCGCCGUUGAUGACGACGACGUCG-A---CAAU----
.((..((((((((((((.(((...((((((....(((...)))..)))))).(((......))).)))))))))))))))..)-)---....---- ( -37.90)
>DroYak_CAF1 8000 93 + 1
GUCCUCAUCGUCAUCAUUUAGGUGCAGGAGAUCAGCCUCAGGUGGCUCCUGAGGCAGC---GCCGCCGACGACGAGGAUGUCACUCCCUGACCACU
((((((.(((((........(((((..(....).((((((((.....)))))))).))---)))...))))).))))))((((.....)))).... ( -40.80)
>DroAna_CAF1 7595 90 + 1
GUCCUCCUCGUCAUCGUUUAGGUGCAGGAGAUCGGCUUCCGGCGGCUCCUGGGGCUGC---GACGUCGCCGACGAAGAGCCCACUCCACUUCC---
(..(((.(((((.......((.(.((((((.(((.(....).))))))))).).))((---(....))).))))).)))..)...........--- ( -32.00)
>DroPer_CAF1 8941 87 + 1
GUCCUCGUCGUCGUCGUUCAAAUGCAGGAGAUCAGCCUCGGGGGGCUCUUGAGGUAAC---GACGACGACGAGGAGGAGGUCACUCC------ACC
.((((((((((((((((((.....(((((.....((((....)))))))))..).)))---))))))))))))))((((....))))------... ( -48.40)
>consensus
GUCCUCGUCGUCAUCAUUCAAAUGCAGGAGAUCAGCCUCGGGCGGCUCCUGAGGCAGC___GACGACGACGACGAGGAGGUCACUCC____C_AC_
.(((((.((((((((.(((.......))))))..((((((((.....))))))))............))))).))))).................. (-25.76 = -24.77 +  -1.00)

alignment

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secondary structure

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Window 4

Location 11,104,838 – 11,104,931
Length 93
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 74.59
Mean single sequence MFE -36.93
Consensus MFE -15.61
Energy contribution -16.41
Covariance contribution 0.81
Combinations/Pair 1.21
Mean z-score -2.19
Structure conservation index 0.42
SVM decision value 0.85
SVM RNA-class probability 0.865442
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11104838 93 - 22407834
AGUGGACAGGGGGUGACAUCCUCGUCAUCGGCGGC---GCUGCCUCAGGAGCCACCUGAGGCUGAUCUCCUGCACCUAAAUGAUGACGAUGAGGAC
........((((....).)))(((((((((..((.---((.((((((((.....)))))))).........)).))....)))))))))....... ( -35.50)
>DroPse_CAF1 8983 87 - 1
GGU------GGAGUGACCUCCUCCUCGUCGUCGUC---GUUACCUCAAGAGCCCCCCGAGGCUGAUCUCCUGCAUUUGAACGACGACGACGAGGAC
...------((((....))))((((((((((((((---((....(((((.((.....((((....))))..)).))))))))))))))))))))). ( -40.80)
>DroGri_CAF1 9045 88 - 1
----AUUG---U-CGACGUCGUCGUCAUCAACGGCGCACAUACCUCAAGAGCCGCCCGAGGCUGAUCUCCUGCAUUUGAAUGACGACGACGAGGAU
----...(---(-(..(((((((((((((((.(((...............)))((..((((....))))..))..))).))))))))))))..))) ( -32.16)
>DroYak_CAF1 8000 93 - 1
AGUGGUCAGGGAGUGACAUCCUCGUCGUCGGCGGC---GCUGCCUCAGGAGCCACCUGAGGCUGAUCUCCUGCACCUAAAUGAUGACGAUGAGGAC
....((((.....)))).((((((((((((((((.---.(.((((((((.....)))))))).).....))))..(.....).)))))))))))). ( -40.70)
>DroAna_CAF1 7595 90 - 1
---GGAAGUGGAGUGGGCUCUUCGUCGGCGACGUC---GCAGCCCCAGGAGCCGCCGGAAGCCGAUCUCCUGCACCUAAACGAUGACGAGGAGGAC
---..............(((((((((((((....)---)).....((((((.((.(....).))..))))))...........))))))))))... ( -31.60)
>DroPer_CAF1 8941 87 - 1
GGU------GGAGUGACCUCCUCCUCGUCGUCGUC---GUUACCUCAAGAGCCCCCCGAGGCUGAUCUCCUGCAUUUGAACGACGACGACGAGGAC
...------((((....))))((((((((((((((---((....(((((.((.....((((....))))..)).))))))))))))))))))))). ( -40.80)
>consensus
_GU_G____GGAGUGACCUCCUCGUCGUCGACGGC___GCUACCUCAAGAGCCACCCGAGGCUGAUCUCCUGCACCUAAACGACGACGACGAGGAC
..................(((((.((((((.((.....((.........((((......))))........)).......)).)))))).))))). (-15.61 = -16.41 +   0.81)

alignment

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secondary structure

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Window 5

Location 11,104,909 – 11,105,004
Length 95
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 84.12
Mean single sequence MFE -35.15
Consensus MFE -22.05
Energy contribution -22.00
Covariance contribution -0.05
Combinations/Pair 1.33
Mean z-score -2.53
Structure conservation index 0.63
SVM decision value -0.05
SVM RNA-class probability 0.507366
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11104909 95 - 22407834
CAACAACAUUCCCUUGCCCACAAGUCUGCCCCACUGUUUGCAUCCCAACGUGCUACAAGC------AGCUGCGUCCGGCAGUGGACAGGGGGUGACAUCCU
.......................(((.(((((.(((((..(..((..(((((((......------))).))))..))..)..)))))))))))))..... ( -32.40)
>DroSec_CAF1 8191 95 - 1
CAACAACAUUCCCUUGCCCACAAGUCUGCCCCACUGUUUGCAUCCCAACGUGCUACAAGC------GGCUGUGUCCGGCAGUGGGCAGGGGGUGACAUCCU
......(((.(((((((((((.....(((((((((((((((((......))))...))))------)).)).)...))))))))))))))))))....... ( -35.00)
>DroSim_CAF1 8449 95 - 1
CAACAACAUUCCCUUGCCCACAAGUCUGCCCCACUGUUUGCAUCCCAACGUGCUACAAGC------GGCUGCGUCCGGCAGUGGACAGGGGGUGACAUCAU
.......................(((.(((((.(((((..(..((..(((((((......------))).))))..))..)..)))))))))))))..... ( -32.40)
>DroEre_CAF1 8318 95 - 1
CAACAACAUUCCCUUGCCCACAAGUCUGCCCCAUUGCUUGCAUCCCAACGUGUUGCAAGC------GGCUGCGUCCGGCAGUGGACAGGGGGUGACAUCCU
......(((.((((((.((((......(((.....(((((((...........)))))))------)))(((.....))))))).)))))))))....... ( -33.00)
>DroYak_CAF1 8071 95 - 1
CAACAACAUUCCUUUGCCCACUAGUCUGCCCCAAUGUUUGCAUCCUAACGUAUUACAAGC------GGCUGCAUCCGGCAGUGGUCAGGGAGUGACAUCCU
......((((((((.(.(((((.((((((.....((((((....(....).....)))))------)...)))...)))))))).)))))))))....... ( -25.30)
>DroPer_CAF1 9012 95 - 1
CAACAAUAUACCGCUGCCCACCAGCCUGCCCCACUGUCUGCAUCCGAAUGUGCUGCAGACGAAGGCGGUUGGGGGCAGCGGU------GGAGUGACCUCCU
.........((((((((((.((((((.(((....((((((((.((....).).))))))))..)))))))))))))))))))------((((....)))). ( -52.80)
>consensus
CAACAACAUUCCCUUGCCCACAAGUCUGCCCCACUGUUUGCAUCCCAACGUGCUACAAGC______GGCUGCGUCCGGCAGUGGACAGGGGGUGACAUCCU
......((((((((.(.((((.............(((..((((......)))).)))..........((((....)))).)))).)))))))))....... (-22.05 = -22.00 +  -0.05)

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 11:01:48 2006