Locus 838

Sequence ID	3R_DroMel_CAF1
Location	2,872,467 – 2,872,707
Length	240
Max. P	0.933506

overview

Window 2

Location	2,872,467 – 2,872,587
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.57
Mean single sequence MFE	-48.15
Consensus MFE	-38.39
Energy contribution	-39.70
Covariance contribution	1.31
Combinations/Pair	1.07
Mean z-score	-2.18
Structure conservation index	0.80
SVM decision value	1.23
SVM RNA-class probability	0.933506
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2872467 120 + 27905053
UGCGGCAAAGUGGCUGCUAGAUAGGGGGCGAGAGGGGGUGUUUGGGGAUGGGUGGGUGUUGGGGGCUUGUGAAAAGCCCUGGCCGCACACAUUUUCCGCGGCAGCUGCUCCCUGAGAAAU
.(((((......)))))....((((((((.((....(.(((..(..((((.(((.(.((..(((.(((.....))))))..))).))).))))..).))).)..))))))))))...... ( -50.40)
>DroSec_CAF1 3670 115 + 1
UGCGGCAAAGUGGCUGCUAGAUGGGGGACGGCAGAGGGGGUUUGUGGAUGCG-----GUUGGGGGCUUGUGAAAAGCCCUGGCCGCACACAUUUUCCGCGGCAGCUGCUCCCUGAGAAAU
.(((((......))))).....(((((.((((.(..(.((...(((..((((-----((..(((.(((.....))))))..))))))..)))...)).)..).)))))))))........ ( -54.00)
>DroSim_CAF1 4051 116 + 1
UGCGGCAAAGUGGCUGCUAGAUGGGGGACGGCAGGGGGGGUUUGUGGAUGCG----GGUUGGGGGCUUGUGAAAAGCCCUGGCCGCACACAUUUUCCGCGGCAGCUGCUCCCUGAGAAAU
.(((((......))))).....(((((.((((.(.((..(..((((..((((----(.(..(((((((.....)))))))).))))))))).)..)).)....)))))))))........ ( -51.40)
>DroEre_CAF1 4616 100 + 1
UGCGGCAAAGUGGCUGCUAGAUAGGGGGCGAGGGGGG----------A----------UGGGGAGUUUCUGAAAAGCCCUGGCCGCACACAUUUUCCGCGGCAGCUGCUCCCUGAGAAAU
.(((((......)))))....(((((((((..((..(----------(----------(((((..((.....))..)))((......))))))..))((....)))))))))))...... ( -36.80)
>consensus
UGCGGCAAAGUGGCUGCUAGAUAGGGGACGACAGGGGGGGUUUGUGGAUGCG_____GUUGGGGGCUUGUGAAAAGCCCUGGCCGCACACAUUUUCCGCGGCAGCUGCUCCCUGAGAAAU
.(((((......)))))....(((((((((((.............................(((((((.....))))))).(((((...........))))).)))))))))))...... (-38.39 = -39.70 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	2,872,507 – 2,872,627
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.24
Mean single sequence MFE	-33.55
Consensus MFE	-29.81
Energy contribution	-29.88
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.37
Structure conservation index	0.89
SVM decision value	0.10
SVM RNA-class probability	0.584824
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2872507 120 - 27905053
CGACUUCCUUACUAACUACGCACGAAAUCAAGUGGGGAAAAUUUCUCAGGGAGCAGCUGCCGCGGAAAAUGUGUGCGGCCAGGGCUUUUCACAAGCCCCCAACACCCACCCAUCCCCAAA
....(((((((((.................))))))))).........((((...(((((((((.....)))).)))))..((((((.....))))))..............)))).... ( -34.23)
>DroSec_CAF1 3710 115 - 1
CGACUUCCUUACUAACUACGCACGAAAUCAAGUGGGGAAAAUUUCUCAGGGAGCAGCUGCCGCGGAAAAUGUGUGCGGCCAGGGCUUUUCACAAGCCCCCAAC-----CGCAUCCACAAA
....(((((((((.................)))))))))..........(((((.(((((((((.....)))).)))))..((((((.....)))))).....-----.)).)))..... ( -34.73)
>DroSim_CAF1 4091 116 - 1
CGACUUCCUUACUAACUACGCACGAAAUCAAGUGGGGAAAAUUUCUCAGGGAGCAGCUGCCGCGGAAAAUGUGUGCGGCCAGGGCUUUUCACAAGCCCCCAACC----CGCAUCCACAAA
....(((((((((.................)))))))))..........(((((.(((((((((.....)))).)))))..((((((.....))))))......----.)).)))..... ( -34.73)
>DroEre_CAF1 4653 103 - 1
CGACUUCCUUACUAACUACGCACGAAAUCAAGUGGGGAAAAUUUCUCAGGGAGCAGCUGCCGCGGAAAAUGUGUGCGGCCAGGGCUUUUCAGAAACUCCCCA----------U-------
...............................(((((((...(((((..((((((..((((((((.(.....).))))).))).)))))).))))).))))))----------)------- ( -30.50)
>consensus
CGACUUCCUUACUAACUACGCACGAAAUCAAGUGGGGAAAAUUUCUCAGGGAGCAGCUGCCGCGGAAAAUGUGUGCGGCCAGGGCUUUUCACAAGCCCCCAAC_____CGCAUCCACAAA
.(.((((((...........(((........)))((((.....))))))))))).(((((((((.....)))).)))))..((((((.....))))))...................... (-29.81 = -29.88 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	2,872,587 – 2,872,707
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.31
Mean single sequence MFE	-33.52
Consensus MFE	-28.85
Energy contribution	-30.85
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.86
SVM decision value	0.65
SVM RNA-class probability	0.812353
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2872587 120 + 27905053
UUUCCCCACUUGAUUUCGUGCGUAGUUAGUAAGGAAGUCGCGUUCAUUCGUUCGCAGCUCUAACGAGCCCCAGCGAAUAUUUAUGAUCAGCACGGGCUCAUGGGCCUCCUCCUAACCACC
......(((........))).((.(((((..((((.((.((..((((..((((((.((((....))))....))))))....))))...)))).((((....)))))))).))))).)). ( -35.30)
>DroSec_CAF1 3785 119 + 1
UUUCCCCACUUGAUUUCGUGCGUAGUUAGUAAGGAAGUCGCGUUCAUUCGUUCGCAGCUCUAACGAGCCCCAGCGAAUAUUUAUGAUCAGCAUGGGCUCACCG-CCCACUCCUCUCCACC
...........((((((.(((.......)))..))))))((..((((..((((((.((((....))))....))))))....))))...)).(((((.....)-))))............ ( -34.80)
>DroSim_CAF1 4167 116 + 1
UUUCCCCACUUGAUUUCGUGCGUAGUUAGUAAGGAAGUCGCGUUCAUUCGUUCGCAGCUCUAACGAGCCCCAGCGAAUAUUUAUGAUCAGCAUGGGCUCAC----CCACUCCUCACCACC
....((((...((((((.(((.......)))..))))))((..((((..((((((.((((....))))....))))))....))))...)).)))).....----............... ( -31.70)
>DroEre_CAF1 4716 117 + 1
UUUCCCCACUUGAUUUCGUGCGUAGUUAGUAAGGAAGUCGCGUUCAUUCGUUCGCAGCUCUAACGAGCCCCAGCGAAUAUUUAUGAUCAGCCUGGGCUCACCG-CCC--CCUUUACCACC
...........((((((.(((.......)))..))))))((..((((..((((((.((((....))))....))))))....))))...))..((((.....)-)))--........... ( -32.30)
>consensus
UUUCCCCACUUGAUUUCGUGCGUAGUUAGUAAGGAAGUCGCGUUCAUUCGUUCGCAGCUCUAACGAGCCCCAGCGAAUAUUUAUGAUCAGCAUGGGCUCACCG_CCCACUCCUCACCACC
....(((....((((((.(((.......)))..))))))((..((((..((((((.((((....))))....))))))....))))...))..)))........................ (-28.85 = -30.85 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:24 2006