Locus 1354

Sequence ID 2L_DroMel_CAF1
Location 3,592,601 – 3,592,790
Length 189
Max. P 0.913397
window2214 window2215

overview

Window 4

Location 3,592,601 – 3,592,692
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.07
Mean single sequence MFE -17.52
Consensus MFE -12.90
Energy contribution -12.77
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -0.97
Structure conservation index 0.74
SVM decision value -0.04
SVM RNA-class probability 0.514403
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3592601 91 - 22407834
------AA-GGCAACACGA--------GGAAGAGAAACACUUGAGUGGCACAUAAAAGUCACAUCGACAACU--UCGAUUGACUAAAGAAAAUAUUGUACAUG-------AACAA-----
------..-.((.((.(((--------(...........)))).)).)).......(((((.(((((.....--))))))))))..........((((.....-------.))))----- ( -15.80)
>DroPse_CAF1 66530 107 - 1
G--AGAGA-GGCAACAUGG--------GGAAGAGAAACACUUGAGUGGCAUAUAAAAGUCACAUCGACAACU--UCGAUUGACUAAAGAAAAUAUUGUACAUGGCGAUGGAACACUGAAC
.--.....-(....)....--------.............((.((((.........(((((.(((((.....--))))))))))........((((((.....))))))...)))).)). ( -18.40)
>DroEre_CAF1 62157 91 - 1
------AA-GGCAACACGA--------GGAAGGGAAACACUUGAGUGGCACAUAAAAGUCACAUCGACAACU--UCGAUUGACUAAAGAAAAUAUUGUACAUG-------AACAA-----
------..-.((.((.(((--------(....(....).)))).)).)).......(((((.(((((.....--))))))))))..........((((.....-------.))))----- ( -18.70)
>DroWil_CAF1 90381 101 - 1
CCAACAUG-GACAACAUCGGCAACAUUGGGGCAGAAACACUUGAGUGGCAUAUAAAAGUCACAUCGACAACUUUUCGAUUGACUAAAGAAAAUAUUGUGUGU------------------
((((.(((-.....))).(....).))))........(((....)))((((((((.(((((.(((((.......))))))))))..........))))))))------------------ ( -18.40)
>DroAna_CAF1 65202 92 - 1
------AAGAGCAACAUGA--------GGAAAAGAAACACUUGAGUGGCAUAUAAAAGUCACAUCGACAACU--UCGAUUGACUAAAGAAAAUAUUGUACAUG-------AACAA-----
------........((((.--------..........(((....))).........(((((.(((((.....--))))))))))...............))))-------.....----- ( -15.40)
>DroPer_CAF1 66784 107 - 1
G--AGAGA-GGCAACAUGG--------GGAAGAGAAACACUUGAGUGGCAUAUAAAAGUCACAUCGACAACU--UCGAUUGACUAAAGAAAAUAUUGUACAUGGCGAUGGAACACUGAAC
.--.....-(....)....--------.............((.((((.........(((((.(((((.....--))))))))))........((((((.....))))))...)))).)). ( -18.40)
>consensus
______AA_GGCAACAUGA________GGAAGAGAAACACUUGAGUGGCAUAUAAAAGUCACAUCGACAACU__UCGAUUGACUAAAGAAAAUAUUGUACAUG_______AACAA_____
..........((((.......................(((....))).........(((((.(((((.......))))))))))..........))))...................... (-12.90 = -12.77 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,592,692 – 3,592,790
Length 98
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 82.05
Mean single sequence MFE -19.02
Consensus MFE -15.70
Energy contribution -15.73
Covariance contribution 0.03
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 1.09
SVM RNA-class probability 0.913397
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3592692 98 - 22407834
UCUCCAACAAUGAUAUUAAA--AAUAACAAUUGUCUUCAGUGGUCUUUAACACCCGCACCGCUGAUAGACAACCAAA---AACAGCAGAG-CAGCA-AAGCAGCA------
....................--........(((((((((((((((..........).)))))))).)))))).....---....((...(-(....-..)).)).------ ( -18.70)
>DroSim_CAF1 63738 89 - 1
UCUCCAACAAUGAUAUUAAA--AAUAACAAUUGUCUUCAGUGGUCUUUAACACCCGCACCGCUGAUAGACAAC-AAA---AACAGCAGAG-CA---------GCA------
....................--........(((((((((((((((..........).)))))))).)))))).-...---....((....-..---------)).------ ( -18.00)
>DroEre_CAF1 62248 96 - 1
UCUCCAACAAUGAUAUUAAA--AAUAACAAUUGUCUUCAGUGGUCUUUAACACCCGCACCGCUGAUAGGCAAC-A----AGGCAGCAAGG-CAGCA-AGGCAGCA------
.((((...............--........(((((((((((((((..........).)))))))).)))))).-.----..((.((...)-).)).-.)).))..------ ( -19.50)
>DroWil_CAF1 90482 104 - 1
GCCUCAACAAUGAUAUUAAAAAAAUAACAAUUGUCUUCAAUGGUCUUUAACACCCGCACCGCUGAUAGACAAC-AGC---AACAACAUGGCCAACA-UGG--CCAACAUGG
((........((.((((.....)))).)).(((((((((.(((((..........).)))).))).)))))).-.))---.......(((((....-.))--)))...... ( -20.50)
>DroYak_CAF1 63534 101 - 1
UCUCCAACAAUGAUAUUAAA--AAUAACAAUUGUCUUCAGUGGUCUUUAACACCCGCACCGCUGAUAGACAAC-AAAAAAAGCAGCAGAG-CAGCAAAGGCAGCA------
.((((...............--........(((((((((((((((..........).)))))))).)))))).-.......((.((...)-).))...)).))..------ ( -20.30)
>DroAna_CAF1 65294 82 - 1
UCGCCAACAAUGAUAUUAAA--AAUAACAAUUGUCUUCAGUGGUCUUUAACACCCGCACCGCUGAUAGACAAC-AAAA--AACA------------------GCA------
..((......((.(((....--.))).)).(((((((((((((((..........).)))))))).)))))).-....--....------------------)).------ ( -17.10)
>consensus
UCUCCAACAAUGAUAUUAAA__AAUAACAAUUGUCUUCAGUGGUCUUUAACACCCGCACCGCUGAUAGACAAC_AAA___AACAGCAGAG_CAGCA_AGG__GCA______
..............................(((((((((((((((..........).)))))))).))))))....................................... (-15.70 = -15.73 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:28 2006