Locus 5798

Sequence ID	2R_DroMel_CAF1
Location	18,353,790 – 18,353,950
Length	160
Max. P	0.766768

overview

Window 5

Location	18,353,790 – 18,353,910
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.36
Mean single sequence MFE	-44.03
Consensus MFE	-38.72
Energy contribution	-38.60
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.63
Structure conservation index	0.88
SVM decision value	0.52
SVM RNA-class probability	0.766768
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18353790 120 - 20766785
AGGAGCCCCAGAAGGGACUGCUGAUGGUGUACGACUUCUGAGGCUCUGUCAGUCGGUAUUCCGGAUAAUUUGGGUUGCUGCUAUUGGCAUUCGUAAAGGCCACAAUGGCCACGCUCAUGU
.((((((.((((((....(((.......)))...)))))).))))))(((((((((((..(((((...)))))..)))))..)))))).........((((.....)))).......... ( -42.20)
>DroSim_CAF1 3946 120 - 1
AGGAGCCCCAGAAGGGACUGCUGAUGGUGUACGACUUCUGAGGCUCCGUCAGGCGAUAUUCCGGAUAAUUCGGGUUACUGCUAUUGGCAUUCGUAAAGGCCACAAUGGCCACGCUCAUGU
.((((((.((((((....(((.......)))...)))))).))))))((((((((.((..(((((...)))))..)).))))..)))).........((((.....)))).......... ( -44.10)
>DroEre_CAF1 3791 120 - 1
AGGAGCCCCAGAAGGGACUGCUGAGUAUGUACGACUUCUGCGGCUCCGUCAGCCGAUACUCCGGAUAAUUCGGGUUACUGCUGUUGGCAUUCGUGAACGCCACAAUGGCCACGCUCAUGU
.((((((.((((((....(((.......)))...)))))).))))))((((((.(..((.(((((...))))))).....).))))))...((((...(((.....)))))))....... ( -41.90)
>DroYak_CAF1 4002 120 - 1
AGGAGCCCCAGAAGGGACUGCUGAGUAUGUAGGACUUCUGCGGCUCCGUCAGUUGAUAUUCCGGAUAAUUCGGGUUACUGCUAUUGGCAUUGGUGAAGGCCACAAUGGCCACGCUCAUGU
.((((((.((((((...((((.......))))..)))))).))))))(.((((......((((((...))))))..))))).....((((.((((..((((.....)))).)))).)))) ( -47.90)
>consensus
AGGAGCCCCAGAAGGGACUGCUGAGGAUGUACGACUUCUGAGGCUCCGUCAGUCGAUAUUCCGGAUAAUUCGGGUUACUGCUAUUGGCAUUCGUAAAGGCCACAAUGGCCACGCUCAUGU
.((((((.((((((....(((.......)))...)))))).))))))((((((.(.....((.((....)).))......).)))))).........((((.....)))).......... (-38.72 = -38.60 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	18,353,830 – 18,353,950
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.83
Mean single sequence MFE	-44.42
Consensus MFE	-34.56
Energy contribution	-35.00
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-1.75
Structure conservation index	0.78
SVM decision value	0.31
SVM RNA-class probability	0.681656
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18353830 120 - 20766785
AAGCGACUCGAUAGGUAUCCACUCAUCAUCUGGGUGCAGCAGGAGCCCCAGAAGGGACUGCUGAUGGUGUACGACUUCUGAGGCUCUGUCAGUCGGUAUUCCGGAUAAUUUGGGUUGCUG
.((((((((((....(((((........((((((.((.......)))))))).((((((((((((((.((............)).))))))).))))..))))))))..)))))))))). ( -47.10)
>DroSim_CAF1 3986 120 - 1
AAGCGACUAGAGAGAUAGCCACUCAUCAUCUGGGUGCAGCAGGAGCCCCAGAAGGGACUGCUGAUGGUGUACGACUUCUGAGGCUCCGUCAGGCGAUAUUCCGGAUAAUUCGGGUUACUG
.((..(((.(((((.......)))...(((((((....((.((((((.((((((....(((.......)))...)))))).)))))).....)).....)))))))...)).)))..)). ( -39.80)
>DroEre_CAF1 3831 120 - 1
AAGCGACUCGAGAUAUAGCCACUCAUCAUGUGCGUGCAGCAGGAGCCCCAGAAGGGACUGCUGAGUAUGUACGACUUCUGCGGCUCCGUCAGCCGAUACUCCGGAUAAUUCGGGUUACUG
.((..(((((((((..((((.(......((((((((((((((...(((.....))).)))))..)))))))))......).))))..)))..(((......))).....))))))..)). ( -44.10)
>DroYak_CAF1 4042 120 - 1
AAGCGACUGGAGAGAUAGCCACUCAUCAUGUGGGUGCAGCAGGAGCCCCAGAAGGGACUGCUGAGUAUGUAGGACUUCUGCGGCUCCGUCAGUUGAUAUUCCGGAUAAUUCGGGUUACUG
...(((((((.......(((((((((...)))))))..)).((((((.((((((...((((.......))))..)))))).)))))).)))))))....((((((...))))))...... ( -46.70)
>consensus
AAGCGACUCGAGAGAUAGCCACUCAUCAUCUGGGUGCAGCAGGAGCCCCAGAAGGGACUGCUGAGGAUGUACGACUUCUGAGGCUCCGUCAGUCGAUAUUCCGGAUAAUUCGGGUUACUG
...(((((.((......((((((((.....))))))..)).((((((.((((((....(((.......)))...)))))).)))))).)))))))....((((((...))))))...... (-34.56 = -35.00 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:40 2006