Locus 788

Sequence ID 2R_DroMel_CAF1
Location 3,755,826 – 3,755,958
Length 132
Max. P 0.990190
window1382 window1383 window1384

overview

Window 2

Location 3,755,826 – 3,755,929
Length 103
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 72.91
Mean single sequence MFE -35.72
Consensus MFE -18.48
Energy contribution -21.07
Covariance contribution 2.59
Combinations/Pair 1.10
Mean z-score -2.30
Structure conservation index 0.52
SVM decision value 1.96
SVM RNA-class probability 0.984003
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3755826 103 + 20766785
GGCGUUGCGGUGGGCAUGGCGUCUGUUCACAUUGUGGCA-GUU--CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGGGAUGCUGAUGCUUUUGC--CGAGCUUCCG
((.(((.(((((((((((((((((((.(((...))))).-...--((((((((((((((....))))))).)))))))))))))).))))))..))--)))))..)). ( -40.30)
>DroSec_CAF1 12527 87 + 1
------------GGCA----GUCUGUUCACAUUGUGGCA-GUU--CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGCGAUGCUGAUGCUUUUGC--CGAGCUUCCG
------------.(((----((........)))))((.(-(((--((((((((((((((....))))))).))))))((((.((....))..))))--.))))).)). ( -28.70)
>DroSim_CAF1 6778 91 + 1
------------GGCAUGGCGUCUGUUCACAUUGUGGCA-GUU--CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGGGAUGCUGAUGCUUUUGC--CGAGCUUCCG
------------((((.((((((....(((...)))(((-.((--((((((((((((((....))))))).))))))))).))).))))))..)))--)......... ( -36.40)
>DroEre_CAF1 12368 93 + 1
GGCGUUGCGGUGGGCAUGGCGUCUGCUCACAUUGUGGCA-GUU--CGUCAAGUGACCUGAAUGUAGGUUAGCUUGAUGGGAUGCUGAUGCUGAUGC------------
.(((((((((((((((.......))))))).....((((-.((--((((((((((((((....))))))).))))))))).))))..))).)))))------------ ( -38.00)
>DroYak_CAF1 5985 105 + 1
GGCGCUGCGGUGGGCAUGGCGUCUGCUCACAUUGAGGCA-GUU--CGUCAAGUGACCUGAAUGUAGGUUAGCUUGAUGGGAUGCUGAAGCUUUUGCUCUGUGCUUCCG
(((((.((((((((((.......))))))).....((((-.((--((((((((((((((....))))))).))))))))).))))........)))...))))).... ( -40.60)
>DroAna_CAF1 12019 99 + 1
UGGGCUUUGGGGGGCAGGAACG--AAGAGCAAUGCCCCAUGUUUGUAUCAAGUGACCUGAAUGUAGGUUAGGUGG-----AUUCUGAGGCAGACGC--AGAGAUAGUG
....(((((.((((((....(.--....)...))))))..((((((.(((..(.((((((.......)))))).)-----....))).)))))).)--))))...... ( -30.30)
>consensus
GGCG_UGCGGUGGGCAUGGCGUCUGUUCACAUUGUGGCA_GUU__CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGGGAUGCUGAUGCUUUUGC__CGAGCUUCCG
............(((((((((((((((........))).......((((((((((((((....))))))).)))))))))))))).)))))................. (-18.48 = -21.07 +   2.59)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,755,859 – 3,755,958
Length 99
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 73.15
Mean single sequence MFE -37.35
Consensus MFE -18.26
Energy contribution -18.71
Covariance contribution 0.45
Combinations/Pair 1.08
Mean z-score -2.49
Structure conservation index 0.49
SVM decision value 2.20
SVM RNA-class probability 0.990190
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3755859 99 + 20766785
GUGGCA-GUU--CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGGGAUGCUGAUGCUUUUGC--CGAGCUUCCGAGGAG--GGUGCAGUGGUGCCCCCAAGGGGG---------
.(((((-(((--((((((((((((((....))))))).)))))))))..((....))..))))--))..(((((..((.(--((..(....)..)))))..)))))--------- ( -42.20)
>DroSec_CAF1 12544 96 + 1
GUGGCA-GUU--CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGCGAUGCUGAUGCUUUUGC--CGAGCUUCCGA---G--GGUGCAGUGGUGCCCCCAAGGGGG---------
.(((((-(..--((((((((((((((....))))))).)))))))....((....))..))))--))..(((((..---(--((.(((....))).)))..)))))--------- ( -36.30)
>DroSim_CAF1 6799 96 + 1
GUGGCA-GUU--CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGGGAUGCUGAUGCUUUUGC--CGAGCUUCCGA---G--GGUGCAGUGGUGCCCCCAAGGGGG---------
.(((((-(((--((((((((((((((....))))))).)))))))))..((....))..))))--))..(((((..---(--((.(((....))).)))..)))))--------- ( -38.30)
>DroEre_CAF1 12401 92 + 1
GUGGCA-GUU--CGUCAAGUGACCUGAAUGUAGGUUAGCUUGAUGGGAUGCUGAUGCUGAUGC-------------------AACGCAGUGGUGCCA-CAAGGGGGUUUAAUGUU
((((((-.((--((((((((((((((....))))))).)))))))))..((((.(((....))-------------------)...))))..)))))-)................ ( -34.20)
>DroYak_CAF1 6018 106 + 1
GAGGCA-GUU--CGUCAAGUGACCUGAAUGUAGGUUAGCUUGAUGGGAUGCUGAAGCUUUUGCUCUGUGCUUCCGA---G--AGUGCAGUGGUGCCA-CAAGGGGGCUUGAGGUU
..((((-.((--((((((((((((((....))))))).))))))))).))))..((((((.((((((..(((....---)--))..).(((....))-)...)))))..)))))) ( -40.80)
>DroAna_CAF1 12050 104 + 1
GCCCCAUGUUUGUAUCAAGUGACCUGAAUGUAGGUUAGGUGG-----AUUCUGAGGCAGACGC--AGAGAUAGUGCUGAUGUCUGGCAGGGGUGGCA-GGAGAGGGAU-AAUG--
..(((...(((((.(((..(((((((....)))))))..)))-----(((((..(.(((((((--((........))).)))))).).))))).)))-))...)))..-....-- ( -32.30)
>consensus
GUGGCA_GUU__CGUCAAGUGACCUGAAAGUAGGUUAGCUUGAUGGGAUGCUGAUGCUUUUGC__CGAGCUUCCGA___G__GGUGCAGUGGUGCCA_CAAGGGGG_________
..((((......((((((((((((((....))))))).)))))))...(((((..((....)).......................))))).))))................... (-18.26 = -18.71 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,755,859 – 3,755,958
Length 99
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 73.15
Mean single sequence MFE -23.43
Consensus MFE -11.04
Energy contribution -11.43
Covariance contribution 0.39
Combinations/Pair 1.07
Mean z-score -2.05
Structure conservation index 0.47
SVM decision value 1.07
SVM RNA-class probability 0.910350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3755859 99 - 20766785
---------CCCCCUUGGGGGCACCACUGCACC--CUCCUCGGAAGCUCG--GCAAAAGCAUCAGCAUCCCAUCAAGCUAACCUACUUUCAGGUCACUUGACG--AAC-UGCCAC
---------((((....)))).......(((..--......(((.(((..--((....))...))).)))..(((((...((((......))))..)))))..--...-)))... ( -25.30)
>DroSec_CAF1 12544 96 - 1
---------CCCCCUUGGGGGCACCACUGCACC--C---UCGGAAGCUCG--GCAAAAGCAUCAGCAUCGCAUCAAGCUAACCUACUUUCAGGUCACUUGACG--AAC-UGCCAC
---------...((..(((.(((....))).))--)---..))......(--(((...((....)).(((..(((((...((((......))))..)))))))--)..-)))).. ( -27.40)
>DroSim_CAF1 6799 96 - 1
---------CCCCCUUGGGGGCACCACUGCACC--C---UCGGAAGCUCG--GCAAAAGCAUCAGCAUCCCAUCAAGCUAACCUACUUUCAGGUCACUUGACG--AAC-UGCCAC
---------((((....)))).......(((..--.---(((((.(((..--((....))...))).)))..(((((...((((......))))..))))).)--)..-)))... ( -25.90)
>DroEre_CAF1 12401 92 - 1
AACAUUAAACCCCCUUG-UGGCACCACUGCGUU-------------------GCAUCAGCAUCAGCAUCCCAUCAAGCUAACCUACAUUCAGGUCACUUGACG--AAC-UGCCAC
................(-(((((....(((..(-------------------((....)))...))).....(((((...((((......))))..)))))..--...-)))))) ( -21.80)
>DroYak_CAF1 6018 106 - 1
AACCUCAAGCCCCCUUG-UGGCACCACUGCACU--C---UCGGAAGCACAGAGCAAAAGCUUCAGCAUCCCAUCAAGCUAACCUACAUUCAGGUCACUUGACG--AAC-UGCCUC
..((.((((....))))-.)).......(((..--.---(((((.((...((((....))))..)).)))..(((((...((((......))))..))))).)--)..-)))... ( -23.20)
>DroAna_CAF1 12050 104 - 1
--CAUU-AUCCCUCUCC-UGCCACCCCUGCCAGACAUCAGCACUAUCUCU--GCGUCUGCCUCAGAAU-----CCACCUAACCUACAUUCAGGUCACUUGAUACAAACAUGGGGC
--....-..........-.(((.((.(((.(((((..(((........))--).)))))...))).((-----(......((((......)))).....)))........))))) ( -17.00)
>consensus
_________CCCCCUUG_GGGCACCACUGCACC__C___UCGGAAGCUCG__GCAAAAGCAUCAGCAUCCCAUCAAGCUAACCUACAUUCAGGUCACUUGACG__AAC_UGCCAC
...................((((.............................((....))............(((((...((((......))))..)))))........)))).. (-11.04 = -11.43 +   0.39)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:25 2006