Locus 6960

Sequence ID	2L_DroMel_CAF1
Location	19,324,159 – 19,324,371
Length	212
Max. P	0.951693

overview

Window 3

Location	19,324,159 – 19,324,270
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.07
Mean single sequence MFE	-35.91
Consensus MFE	-32.36
Energy contribution	-32.92
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.90
SVM decision value	0.15
SVM RNA-class probability	0.609276
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19324159 111 - 22407834
---------CCCAGCUCCCAGUGGCCAGCUUGGCCAUUUAGUGGCUGCCAGUCACGCUAUGAUUUGACCCACUUUUAUUGGUUCCAAAUAAGCCGACACGUAAUGAGCUCAAGGCUUAGC
---------..((((..(.(((((((.....)))))))..)..))))...(((..(((...(((((..(((.......)))...))))).))).)))......(((((.....))))).. ( -30.70)
>DroSec_CAF1 16676 111 - 1
---------CGCAGCUCCCAGUGGCCAGCUUGGCCAUUUAGUGGCUGCCAGUCACGCUAUGAUUUGACCCACUUUUAUUGGGUCCAAAUAAGCCGACACGUAAUGAGCUCAAGGCUUAGC
---------.(((((..(.(((((((.....)))))))..)..)))))..(((..(((...((((((((((.......))))).))))).))).)))......(((((.....))))).. ( -40.90)
>DroSim_CAF1 18505 111 - 1
---------CCCAGCUCCCAGUGGCCAGCUUGGCCAUUUAGUGGAUGCCAGUCACGCUAUGAUUUGACCCACUUUUAUUGGGUCCAAAUAAGCCGACACGUAAUGAGCUCAAGGCUUAGC
---------....(((((((((((((.....)))))))..).))).))..(((..(((...((((((((((.......))))).))))).))).)))......(((((.....))))).. ( -35.10)
>DroEre_CAF1 15606 120 - 1
UCCUCGAUCCCCAGCUCCCAGUGGCCGGCUUGGCCAUUUAGUGGCUGCCAGUCACGCUAUGAUUUGACCCACUUUUAUUGGGACCGAAUAAGCCGACGCGUAAUGAGCUCAAGGCUUAGC
...(((.((((........(((((..(((..((((((...))))))))).((((..........)))))))))......)))).))).((((((...((.......))....)))))).. ( -36.94)
>consensus
_________CCCAGCUCCCAGUGGCCAGCUUGGCCAUUUAGUGGCUGCCAGUCACGCUAUGAUUUGACCCACUUUUAUUGGGUCCAAAUAAGCCGACACGUAAUGAGCUCAAGGCUUAGC
...........((((..(.(((((((.....)))))))..)..))))...(((..(((...((((((((((.......))))).))))).))).)))......(((((.....))))).. (-32.36 = -32.92 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	19,324,239 – 19,324,331
Length	92
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.13
Mean single sequence MFE	-36.65
Consensus MFE	-27.94
Energy contribution	-27.63
Covariance contribution	-0.31
Combinations/Pair	1.14
Mean z-score	-2.14
Structure conservation index	0.76
SVM decision value	1.37
SVM RNA-class probability	0.947585
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19324239 92 + 22407834
UAAAUGGCCAAGCUGGCCACUGGGAGCUGGG----------------------------AAUCGGGAGUUAGCAGCUGAGAGAUGCUGGAUGCAUCGAGACCCCCAGUGGGGACAUAAAU
.....((((.....))))(((((((((((..----------------------------((.(....)))..)))))....(((((.....)))))......))))))(....)...... ( -34.00)
>DroSec_CAF1 16756 92 + 1
UAAAUGGCCAAGCUGGCCACUGGGAGCUGCG----------------------------AAUCGGGAGUUAGCGGCUGAGAGAUGCUGGAUGCAUUGAGACCCCCAUUGGGGACAUAAAU
....(((((.....))))).((((((((((.----------------------------...(....)...))))))....(((((.....)))))......)))).((....))..... ( -31.50)
>DroSim_CAF1 18585 92 + 1
UAAAUGGCCAAGCUGGCCACUGGGAGCUGGG----------------------------AAUCGGGAGUUAGCAGCUGAGAGAUGCUGGAUGCAUCGAGACCCCCAGUGGGGACAUAAAU
.....((((.....))))(((((((((((..----------------------------((.(....)))..)))))....(((((.....)))))......))))))(....)...... ( -34.00)
>DroEre_CAF1 15686 120 + 1
UAAAUGGCCAAGCCGGCCACUGGGAGCUGGGGAUCGAGGAUCGGGAAUCGGCAACCGGGAACCGGGAGUUAGCAGCUAACCGAUGUUGGACGCAUCGAGACCCCCAGUGGGGCCAUAAAU
...((((((.......(((((((((((((((..(((.....)))...))(((..((((...))))..)))..)))))...((((((.....)))))).....)))))))))))))).... ( -47.11)
>consensus
UAAAUGGCCAAGCUGGCCACUGGGAGCUGGG____________________________AAUCGGGAGUUAGCAGCUGAGAGAUGCUGGAUGCAUCGAGACCCCCAGUGGGGACAUAAAU
.....((((.....))))(((((((((((...........................................)))))....(((((.....)))))......))))))(....)...... (-27.94 = -27.63 +  -0.31)

alignment

secondary structure

dotplot

Window 5

Location	19,324,239 – 19,324,331
Length	92
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.13
Mean single sequence MFE	-31.26
Consensus MFE	-22.59
Energy contribution	-23.15
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.21
Structure conservation index	0.72
SVM decision value	1.41
SVM RNA-class probability	0.951693
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19324239 92 - 22407834
AUUUAUGUCCCCACUGGGGGUCUCGAUGCAUCCAGCAUCUCUCAGCUGCUAACUCCCGAUU----------------------------CCCAGCUCCCAGUGGCCAGCUUGGCCAUUUA
.............(((((((((..((......((((........)))).....))..))))----------------------------))))).....(((((((.....))))))).. ( -28.30)
>DroSec_CAF1 16756 92 - 1
AUUUAUGUCCCCAAUGGGGGUCUCAAUGCAUCCAGCAUCUCUCAGCCGCUAACUCCCGAUU----------------------------CGCAGCUCCCAGUGGCCAGCUUGGCCAUUUA
......(.((((....)))).)...((((.....)))).....(((.((............----------------------------.)).)))...(((((((.....))))))).. ( -23.22)
>DroSim_CAF1 18585 92 - 1
AUUUAUGUCCCCACUGGGGGUCUCGAUGCAUCCAGCAUCUCUCAGCUGCUAACUCCCGAUU----------------------------CCCAGCUCCCAGUGGCCAGCUUGGCCAUUUA
.............(((((((((..((......((((........)))).....))..))))----------------------------))))).....(((((((.....))))))).. ( -28.30)
>DroEre_CAF1 15686 120 - 1
AUUUAUGGCCCCACUGGGGGUCUCGAUGCGUCCAACAUCGGUUAGCUGCUAACUCCCGGUUCCCGGUUGCCGAUUCCCGAUCCUCGAUCCCCAGCUCCCAGUGGCCGGCUUGGCCAUUUA
....(((((((((((((((((.((((.(.(((....((((((.(((((..(((.....)))..)))))))))))....))).)))))......))))))))))).......))))))... ( -45.21)
>consensus
AUUUAUGUCCCCACUGGGGGUCUCGAUGCAUCCAGCAUCUCUCAGCUGCUAACUCCCGAUU____________________________CCCAGCUCCCAGUGGCCAGCUUGGCCAUUUA
............(((((((((...(((((.....))))).......((........))...................................)))))))))((((.....))))..... (-22.59 = -23.15 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	19,324,270 – 19,324,371
Length	101
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.77
Mean single sequence MFE	-36.65
Consensus MFE	-31.31
Energy contribution	-32.62
Covariance contribution	1.31
Combinations/Pair	1.19
Mean z-score	-2.01
Structure conservation index	0.85
SVM decision value	1.17
SVM RNA-class probability	0.925332
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19324270 101 + 22407834
-------------------AAUCGGGAGUUAGCAGCUGAGAGAUGCUGGAUGCAUCGAGACCCCCAGUGGGGACAUAAAUCCUUACGCUGCAGUUGAAAAACAAUUUUCCCCGGGUAUGC
-------------------..(((((.....(((((((((.(((((.....)))))....((((....)))).........)))).))))).(((....))).......)))))...... ( -36.60)
>DroSec_CAF1 16787 101 + 1
-------------------AAUCGGGAGUUAGCGGCUGAGAGAUGCUGGAUGCAUUGAGACCCCCAUUGGGGACAUAAAUCCUUUCGCUGCAGUUGAAAAACAAUUUUACCCGGGUAUGC
-------------------..(((((.....(((((.(((((((((.....)))).....((((....)))).........)))))))))).(((....))).......)))))...... ( -34.10)
>DroSim_CAF1 18616 101 + 1
-------------------AAUCGGGAGUUAGCAGCUGAGAGAUGCUGGAUGCAUCGAGACCCCCAGUGGGGACAUAAAUCCUUACGCUGCAGUUGAAAAACAAUUUUGCCCGGGUAUGC
-------------------..(((((.....(((((((((.(((((.....)))))....((((....)))).........)))).))))).(((....))).......)))))...... ( -36.50)
>DroEre_CAF1 15726 120 + 1
UCGGGAAUCGGCAACCGGGAACCGGGAGUUAGCAGCUAACCGAUGUUGGACGCAUCGAGACCCCCAGUGGGGCCAUAAAUCCUUACGCUGCAGUUGGAAAACAAUUUUCGCCGGGUAUGC
..........((((((.((...((..((((.(((((....((((((.....)))))).(.((((....)))).)............))))).(((....)))))))..)))).))).))) ( -39.40)
>consensus
___________________AAUCGGGAGUUAGCAGCUGAGAGAUGCUGGAUGCAUCGAGACCCCCAGUGGGGACAUAAAUCCUUACGCUGCAGUUGAAAAACAAUUUUCCCCGGGUAUGC
.....................(((((.....(((((((((.(((((.....)))))....((((....)))).........)))).))))).(((....))).......)))))...... (-31.31 = -32.62 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:03 2006