Locus 6077

Sequence ID	2R_DroMel_CAF1
Location	19,125,682 – 19,125,818
Length	136
Max. P	0.978013

overview

Window 7

Location	19,125,682 – 19,125,799
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	85.55
Mean single sequence MFE	-23.98
Consensus MFE	-17.28
Energy contribution	-17.08
Covariance contribution	-0.20
Combinations/Pair	1.21
Mean z-score	-1.74
Structure conservation index	0.72
SVM decision value	0.20
SVM RNA-class probability	0.633076
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19125682 117 + 20766785
ACAAACGCAGCUCUUAAGAUGUAUUUAUGGCGCCACUGAAAGCUUUUCAAGCUUUCGCUUGCAUUUCCUAACGACCAGCUUUUUAUACCCUUAAAAGGGGGUAUUACGGAAUUAGUA
......(((((................((....))..(((((((.....))))))))).)))..((((.....(((..(((((((......))))))).))).....))))...... ( -25.90)
>DroSec_CAF1 9925 116 + 1
ACAAACACAUCUCUUAAUAUGUAUUUAUGGCGCCACUGAAAGCUUUUCAAGCUUUCGCUUGCAUUUCCUAAGCACUAGCUUUUUAUACCCUUAA-AGGGGGUAUUACACAAUUAGUA
.............(((((.((((.....(((......(((((((.....)))))))(((((.......)))))....)))....(((((((...-..)))))))))))..))))).. ( -24.40)
>DroSim_CAF1 10040 116 + 1
ACAAACGCAGCUCUUAAUAUUUAUUUAUGGCGCCACUGAAAGCUUUUCAAGCUUUCGCUUGCAUUUCCUAAGCACUAGCUUUUUAUACCCUUAA-AGGGAGUAUUAUACAAUUAGUA
......((.(((..(((.......))).)))((...((((((((.....))))))))...)).........))(((((......(((((((...-.))).)))).......))))). ( -22.52)
>DroEre_CAF1 14700 114 + 1
ACCAACGCAGCUCUAAAUAUGUACUUAUGGCGCCACCAAAAGCUUUUCAAGCUUUCGCUUGCAUUUU-UAACCUCUAGCUUUU-AUACCCUUAA-CUAGGGUAUUACACAAUAAGCG
.....(((((((.((((.(((((.....((((......((((((.....))))))))))))))).))-))......))))...-(((((((...-..)))))))..........))) ( -23.70)
>DroYak_CAF1 15352 109 + 1
ACCAACGCAGCUCUAAUUAUGUAUUUAUGGCGCCACCAAAAGCUUUUCAAGCUUUCGUAUGCAUUUU-------CCAGCUUUUGAUACCCUUAA-UGAGGGUAUUACACAUUUAGUA
......((((((......((((((...(((.....)))((((((.....))))))...))))))...-------..))))..((((((((((..-.))))))))))........)). ( -23.40)
>consensus
ACAAACGCAGCUCUUAAUAUGUAUUUAUGGCGCCACUGAAAGCUUUUCAAGCUUUCGCUUGCAUUUCCUAACCACUAGCUUUUUAUACCCUUAA_AGGGGGUAUUACACAAUUAGUA
......((.......................((...((((((((.....))))))))...))......................(((((((......)))))))..........)). (-17.28 = -17.08 +  -0.20)

alignment

secondary structure

dotplot

Window 8

Location	19,125,682 – 19,125,799
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	85.55
Mean single sequence MFE	-30.90
Consensus MFE	-21.26
Energy contribution	-21.50
Covariance contribution	0.24
Combinations/Pair	1.12
Mean z-score	-2.51
Structure conservation index	0.69
SVM decision value	1.04
SVM RNA-class probability	0.904603
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19125682 117 - 20766785
UACUAAUUCCGUAAUACCCCCUUUUAAGGGUAUAAAAAGCUGGUCGUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCUUUCAGUGGCGCCAUAAAUACAUCUUAAGAGCUGCGUUUGU
..(((((.((((.((((((........)))))).....)).))..))))).(((((((.(((((((((.....))))))).(((....)))...............))))))))).. ( -30.10)
>DroSec_CAF1 9925 116 - 1
UACUAAUUGUGUAAUACCCCCU-UUAAGGGUAUAAAAAGCUAGUGCUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCUUUCAGUGGCGCCAUAAAUACAUAUUAAGAGAUGUGUUUGU
.............((((((...-....)))))).....((((.((...(((.....(((((....))))).....))).)).))))...((((((((((........)))))))))) ( -32.30)
>DroSim_CAF1 10040 116 - 1
UACUAAUUGUAUAAUACUCCCU-UUAAGGGUAUAAAAAGCUAGUGCUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCUUUCAGUGGCGCCAUAAAUAAAUAUUAAGAGCUGCGUUUGU
.............((((((...-....))))))...((((....))))...(((((((.(((((((((.....))))))).(((....)))...............))))))))).. ( -26.60)
>DroEre_CAF1 14700 114 - 1
CGCUUAUUGUGUAAUACCCUAG-UUAAGGGUAU-AAAAGCUAGAGGUUA-AAAAUGCAAGCGAAAGCUUGAAAAGCUUUUGGUGGCGCCAUAAGUACAUAUUUAGAGCUGCGUUGGU
.((((((.((((.(((((((..-...)))))))-....((((((((((.-......(((((....)))))...)))))))))).)))).))))))...................... ( -36.20)
>DroYak_CAF1 15352 109 - 1
UACUAAAUGUGUAAUACCCUCA-UUAAGGGUAUCAAAAGCUGG-------AAAAUGCAUACGAAAGCUUGAAAAGCUUUUGGUGGCGCCAUAAAUACAUAAUUAGAGCUGCGUUGGU
..((((.(((((((((((((..-...))))))).......(((-------....(((...((((((((.....))))))))...))))))....)))))).))))............ ( -29.30)
>consensus
UACUAAUUGUGUAAUACCCCCU_UUAAGGGUAUAAAAAGCUAGUGCUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCUUUCAGUGGCGCCAUAAAUACAUAUUAAGAGCUGCGUUUGU
.............((((((........))))))..................(((((((.(((((((((.....))))))).(((....)))...............))))))))).. (-21.26 = -21.50 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	19,125,722 – 19,125,818
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	79.33
Mean single sequence MFE	-22.43
Consensus MFE	-13.42
Energy contribution	-14.10
Covariance contribution	0.68
Combinations/Pair	1.19
Mean z-score	-2.28
Structure conservation index	0.60
SVM decision value	1.32
SVM RNA-class probability	0.942234
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19125722 96 + 20766785
AGCUUUUCAAGCUUUCGCUUGCAUUUCCUAACGACCAGCUUUUUAUACCCUUAAAAGGGGGUAUUACGGAAUUAGUAAGAGCUUUACAAAGCAGUG
.(((((..(((((((..((.....((((.....(((..(((((((......))))))).))).....))))..))..)))))))...))))).... ( -27.40)
>DroSec_CAF1 9965 95 + 1
AGCUUUUCAAGCUUUCGCUUGCAUUUCCUAAGCACUAGCUUUUUAUACCCUUAA-AGGGGGUAUUACACAAUUAGUAAGAGCUUUGCAACGCAGUG
.((....(((((....)))))..........(((..(((((((.(((((((...-..)))))))............))))))).)))...)).... ( -24.52)
>DroSim_CAF1 10080 95 + 1
AGCUUUUCAAGCUUUCGCUUGCAUUUCCUAAGCACUAGCUUUUUAUACCCUUAA-AGGGAGUAUUAUACAAUUAGUAAUAGCUUUGCAACGUGGUG
((((.....)))).(((((((((....(((...(((((......(((((((...-.))).)))).......)))))..)))...))))).)))).. ( -18.12)
>DroEre_CAF1 14740 83 + 1
AGCUUUUCAAGCUUUCGCUUGCAUUUU-UAACCUCUAGCUUUU-AUACCCUUAA-CUAGGGUAUUACACAAUAAGCGAGAA--------AGCAG--
.(((((((((((....)))))......-.........((((..-(((((((...-..)))))))........))))..)))--------)))..-- ( -21.90)
>DroYak_CAF1 15392 88 + 1
AGCUUUUCAAGCUUUCGUAUGCAUUUU-------CCAGCUUUUGAUACCCUUAA-UGAGGGUAUUACACAUUUAGUAAGAACUUUGUAAAGCAAUA
.(((((.((((..(((.(((((.....-------...))...((((((((((..-.))))))))))........))).))).)))).))))).... ( -20.20)
>consensus
AGCUUUUCAAGCUUUCGCUUGCAUUUCCUAACCACUAGCUUUUUAUACCCUUAA_AGGGGGUAUUACACAAUUAGUAAGAGCUUUGCAAAGCAGUG
.((....(((((....)))))...............(((((((.(((((((......)))))))............))))))).......)).... (-13.42 = -14.10 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	19,125,722 – 19,125,818
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	79.33
Mean single sequence MFE	-22.90
Consensus MFE	-15.48
Energy contribution	-16.84
Covariance contribution	1.36
Combinations/Pair	1.22
Mean z-score	-2.38
Structure conservation index	0.68
SVM decision value	1.80
SVM RNA-class probability	0.978013
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19125722 96 - 20766785
CACUGCUUUGUAAAGCUCUUACUAAUUCCGUAAUACCCCCUUUUAAGGGUAUAAAAAGCUGGUCGUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCU
....(((((((((.....))))...((((...((((((........))))))....(((.....))).))))...(((((....))))).))))). ( -24.90)
>DroSec_CAF1 9965 95 - 1
CACUGCGUUGCAAAGCUCUUACUAAUUGUGUAAUACCCCCU-UUAAGGGUAUAAAAAGCUAGUGCUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCU
....((...(((.((((..(((.......)))((((((...-....))))))....))))..)))..........(((((....)))))....)). ( -24.70)
>DroSim_CAF1 10080 95 - 1
CACCACGUUGCAAAGCUAUUACUAAUUGUAUAAUACUCCCU-UUAAGGGUAUAAAAAGCUAGUGCUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCU
..((.....(((.((((..(((.....)))..((((((...-....))))))....))))..)))...)).....(((((....)))))....... ( -21.60)
>DroEre_CAF1 14740 83 - 1
--CUGCU--------UUCUCGCUUAUUGUGUAAUACCCUAG-UUAAGGGUAU-AAAAGCUAGAGGUUA-AAAAUGCAAGCGAAAGCUUGAAAAGCU
--..(((--------((...((((...((...(((((((..-...)))))))-....))...))))..-......(((((....))))).))))). ( -25.10)
>DroYak_CAF1 15392 88 - 1
UAUUGCUUUACAAAGUUCUUACUAAAUGUGUAAUACCCUCA-UUAAGGGUAUCAAAAGCUGG-------AAAAUGCAUACGAAAGCUUGAAAAGCU
....(((((.((((((....)))...(((((.(((((((..-...))))))).....((...-------.....))))))).....))).))))). ( -18.20)
>consensus
CACUGCUUUGCAAAGCUCUUACUAAUUGUGUAAUACCCCCU_UUAAGGGUAUAAAAAGCUAGUGCUUAGGAAAUGCAAGCGAAAGCUUGAAAAGCU
....(((((....((((..(((.....)))..((((((........))))))....))))...............(((((....))))).))))). (-15.48 = -16.84 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:15 2006