Locus 2235

Sequence ID 2R_DroMel_CAF1
Location 8,260,626 – 8,260,763
Length 137
Max. P 0.974458
window3680 window3681 window3682

overview

Window 0

Location 8,260,626 – 8,260,723
Length 97
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 75.91
Mean single sequence MFE -31.85
Consensus MFE -14.50
Energy contribution -15.33
Covariance contribution 0.84
Combinations/Pair 1.20
Mean z-score -1.90
Structure conservation index 0.46
SVM decision value 0.05
SVM RNA-class probability 0.557500
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8260626 97 + 20766785
----AAA--GGGAGUGGGGUCUUUUGG-GUGGUUGGGUGGCUGGUGGCUGUGGGGUGGCUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGU
----.((--((((......))))))..-.......(((((((((..(((((..(((.((((.(......).)))).))).)))))..))....))).))))... ( -37.10)
>DroVir_CAF1 67546 88 + 1
GCUUUGGGGCUGUGUGGGGGCUUUUGUUGUUGUU-----GUUGUUU--------GUUG-UGGGUGCAG--GCAGUAGCCAACAGCUGUUGACAGCCGCACCAGU
(((.((.((((((.(((.((((...((((..(((-----(((((((--------((..-.....))))--)))))))))))))))).))))))))).))..))) ( -30.30)
>DroSec_CAF1 47862 82 + 1
----AAA--GGGAGUGGGGACUUUUGG-GUGGCUGG---------------GGGGUGGCUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGU
----...--((((((....)))))).(-((((((.(---------------..((..((((.....((((......)))).))))..))..).))).))))... ( -31.90)
>DroSim_CAF1 50205 79 + 1
----AAA--GGGAGUGGGAUCUUUUGG-GUGGCUGG------------------GUGGUUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGU
----.((--((((......))))))((-(((.((((------------------(..((((.....((((......)))).))))..))..))).))).))... ( -27.80)
>DroEre_CAF1 47837 87 + 1
----AAU--GGGAGUGGGCUCUGUUGG-GUGGCUGGGUGGUU----------GGGUGGCUGGGAGGAGGUGCAGUGGCCAACAGCUGUCGACAGGCGCACCAGU
----...--..(.(((.((.((((((.-(..((((..(((((----------(.(((.((......)).)))..)))))).))))..))))))))).))))... ( -33.50)
>DroYak_CAF1 49805 86 + 1
----AAG--GGGAGUGGGGUCUGUUGG-GUGACUGGGUGGCU----------GGGUGG-UGGGAGGUGGUGCAGUGGCCAACAGCUGUCGACAGGCGCACCAGU
----...--((.....(.(((((((((-....)).((..(((----------(..(((-(.(..(......)..).)))).))))..))))))))).).))... ( -30.50)
>consensus
____AAA__GGGAGUGGGGUCUUUUGG_GUGGCUGG___G_U__________GGGUGGCUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGU
...........(.(((.(.(((.((((...(((((..................(((.((((.(......).)))).)))..))))).)))).)))).))))... (-14.50 = -15.33 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 8,260,626 – 8,260,723
Length 97
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.91
Mean single sequence MFE -18.55
Consensus MFE -15.04
Energy contribution -14.98
Covariance contribution -0.05
Combinations/Pair 1.17
Mean z-score -1.86
Structure conservation index 0.81
SVM decision value 1.73
SVM RNA-class probability 0.974458
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8260626 97 - 20766785
ACUGGUGCGCCUGUCGGCAGCUGUUGGCCACUGCACCACCUCCCAGCCACCCCACAGCCACCAGCCACCCAACCAC-CCAAAAGACCCCACUCCC--UUU----
.((((((.(((....))).(((((((((.................))))....)))))))))))............-..................--...---- ( -22.23)
>DroVir_CAF1 67546 88 - 1
ACUGGUGCGGCUGUCAACAGCUGUUGGCUACUGC--CUGCACCCA-CAAC--------AAACAAC-----AACAACAACAAAAGCCCCCACACAGCCCCAAAGC
...((((((((.((((((....))))))....))--).)))))..-....--------.......-----.................................. ( -20.60)
>DroSec_CAF1 47862 82 - 1
ACUGGUGCGCCUGUCGGCAGCUGUUGGCCACUGCACCACCUCCCAGCCACCCC---------------CCAGCCAC-CCAAAAGUCCCCACUCCC--UUU----
..(((((((...((((((....))))))...)))))))...............---------------........-..................--...---- ( -16.50)
>DroSim_CAF1 50205 79 - 1
ACUGGUGCGCCUGUCGGCAGCUGUUGGCCACUGCACCACCUCCCAACCAC------------------CCAGCCAC-CCAAAAGAUCCCACUCCC--UUU----
..(((((((...((((((....))))))...)))))))............------------------........-..................--...---- ( -16.50)
>DroEre_CAF1 47837 87 - 1
ACUGGUGCGCCUGUCGACAGCUGUUGGCCACUGCACCUCCUCCCAGCCACCC----------AACCACCCAGCCAC-CCAACAGAGCCCACUCCC--AUU----
...((((((...((((((....))))))...))))))...............----------..............-......(((....)))..--...---- ( -17.00)
>DroYak_CAF1 49805 86 - 1
ACUGGUGCGCCUGUCGACAGCUGUUGGCCACUGCACCACCUCCCA-CCACCC----------AGCCACCCAGUCAC-CCAACAGACCCCACUCCC--CUU----
..(((((((...((((((....))))))...))))))).......-......----------.........(((..-......))).........--...---- ( -18.50)
>consensus
ACUGGUGCGCCUGUCGACAGCUGUUGGCCACUGCACCACCUCCCAGCCACCC__________A_C___CCAGCCAC_CCAAAAGACCCCACUCCC__UUU____
...((((((...((((((....))))))...))))))................................................................... (-15.04 = -14.98 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,260,645 – 8,260,763
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 81.10
Mean single sequence MFE -47.35
Consensus MFE -32.83
Energy contribution -32.67
Covariance contribution -0.16
Combinations/Pair 1.33
Mean z-score -2.78
Structure conservation index 0.69
SVM decision value 1.21
SVM RNA-class probability 0.931208
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8260645 118 + 20766785
GGGUGGUUGGGUGGCUGGUGGCUGUGGGGUGGCUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGUUGCCCGAAAUAGCGCCUUGGGUGGGAAAAUCUUGGGGCUG
..((..(((((..((((((((((((..(((.((((.(......).)))).))).))))).(((....))).)))))))..)))))....))((((..((.........))..)))).. ( -60.40)
>DroSec_CAF1 47881 103 + 1
GGGUGGCUGG---------------GGGGUGGCUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGUUGCCCGAAAUAGCGACUUGGGUGGGAAAAUCUUGGGGCUG
(((..(((((---------------...(((.(((...((..((...((.....)).))..))..))).))).)))))..)))....((((..((.((((......)))).)).)))) ( -44.60)
>DroSim_CAF1 50224 100 + 1
GGGUGGCUGG------------------GUGGUUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGUUGCCCGAAAUAGCGCCUUGGGUGGGAAAAUCUUGGGGCUG
(((..(((((------------------(((.(((...((..((...((.....)).))..))..))).))).)))))..)))....((((.(((.((((......)))).))))))) ( -45.60)
>DroEre_CAF1 47856 105 + 1
GGGUGGCUGGGUGGUU----------GGGUGGCUGGGAGGAGGUGCAGUGGCCAACAGCUGUCGACAGGCGCACCAGUUGCCCCAAAUAGCGCCUUGGGUGGGAAAAUCUUGGGC---
(((..(((((((((((----------((.(.((((.(......).)))).))))))..(((....))).))).)))))..)))........((((.((((......)))).))))--- ( -43.90)
>DroYak_CAF1 49824 104 + 1
GGGUGACUGGGUGGCU----------GGGUGG-UGGGAGGUGGUGCAGUGGCCAACAGCUGUCGACAGGCGCACCAGUUGCCCGAAAUAGCGCCUUGGGUGGGAAAAUCUUGGGC---
(((..((((((((.((----------(..(((-..(....((((......))))....)..))).))).))).)))))..)))........((((.((((......)))).))))--- ( -45.70)
>DroAna_CAF1 50061 91 + 1
GGGCGACUGG------------------GCGACUGGGC---GGAGUGGGGGUCAACAGCUGCCGACAGGCGCACCAGUUGCCCGAAAUAGCUUCUUGGGUGG------CUUGGGUGGC
((((((((((------------------(((.((((((---((..((........)).)))))..))).))).))))))))))......(((.((..((...------))..)).))) ( -43.90)
>consensus
GGGUGGCUGG________________GGGUGGCUGGGAGGUGGUGCAGUGGCCAACAGCUGCCGACAGGCGCACCAGUUGCCCGAAAUAGCGCCUUGGGUGGGAAAAUCUUGGGGCUG
((((((((((.................(((.((((.(......).)))).)))....((.(((....))))).)))))))))).........(((.((((......)))).))).... (-32.83 = -32.67 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:33 2006