Locus 3330

Sequence ID	3L_DroMel_CAF1
Location	9,773,920 – 9,774,037
Length	117
Max. P	0.785754

overview

Window 3

Location	9,773,920 – 9,774,013
Length	93
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	73.86
Mean single sequence MFE	-30.92
Consensus MFE	-18.53
Energy contribution	-19.23
Covariance contribution	0.70
Combinations/Pair	1.33
Mean z-score	-1.48
Structure conservation index	0.60
SVM decision value	0.49
SVM RNA-class probability	0.757214
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9773920 93 - 23771897
UCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGCGUCCAGAUCGCUGUCGGCACCGGCUAAUAAAAAUCGUGGAUACAAUG-----------UA
.......((((((.((((((.(.....).)))))).))))))(..(((((((...(((..((....))..)))...))).))))..)....-----------.. ( -28.60)
>DroSec_CAF1 68439 93 - 1
UCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGGGUCCAGGUCGCUGUCGGCACCGGCUGAGAAAAAUCGUGGAUACAAUG-----------UA
....(((((((((.((((((.(.....).)))))).)))))))))((((.(....(.(((((....))))).).....).)))).......-----------.. ( -35.40)
>DroSim_CAF1 70545 93 - 1
UCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGGGUCCAGGUCGCUGUCGGCACCGGCUGAGAAAAAUCGUGGAUACAAGG-----------UA
.((((((((((((.((((((.(.....).)))))).)))))))))((((.(....(.(((((....))))).).....).))))....)))-----------.. ( -36.80)
>DroEre_CAF1 68822 99 - 1
UCCUCCUCCUCAAACUCCUGCACGAACUGCAGCGGAUUGAGAGCGUCCAGAUCGCUGUCGGCACCGGCUGCGAAAUAUCAUGGAUACAAUGUGGAU-----GUC
........(((((.((.(((((.....))))).)).))))).(((((((.(((((.((((....)))).)))).......((....)).).)))))-----)). ( -33.90)
>DroYak_CAF1 79493 102 - 1
UCCUCCUCCUCAAACUCCUGAACGAACUGCAGGGGAUUGAGUGCGUCCAGAUCGCUAUCGGCACCGGCUGGGAAAAAUCAUGGAUACAG--UGGAUACAAAGUU
...(((.((((((.((((((.........)))))).)))))((..(((((((.....(((((....))))).....))).))))..)))--.)))......... ( -30.00)
>DroAna_CAF1 69575 79 - 1
UCGCUCUCUU---UCUCCUCCACGUAUUGGAUGGGAUCCAGAGGGUCCAUUUCGCUGAUGGCU------AA--AGGGAUAUGAAUAUAAG--------------
..(((((((.---((((.((((.....)))).))))...))))))).(((.((.((.......------..--)).)).)))........-------------- ( -20.80)
>consensus
UCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGCGUCCAGAUCGCUGUCGGCACCGGCUGAGAAAAAUCAUGGAUACAAUG___________UA
........(((((.((((((.........)))))).)))))...((((((((.....(((((....))))).....))).)))))................... (-18.53 = -19.23 +   0.70)

alignment

secondary structure

dotplot

Window 4

Location	9,773,939 – 9,774,037
Length	98
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	79.25
Mean single sequence MFE	-39.24
Consensus MFE	-23.49
Energy contribution	-24.97
Covariance contribution	1.48
Combinations/Pair	1.23
Mean z-score	-1.89
Structure conservation index	0.60
SVM decision value	0.57
SVM RNA-class probability	0.785754
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9773939 98 - 23771897
CGCAGCGGUUCCGAUAUCGAGUUAUCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGCGUCCAGAUCGCUGUCGGCACCGGCUAAUAA
...((((((.((((((.(((........(.(((((((.((((((.(.....).)))))).))))))).)......))).)))))).))).)))..... ( -36.94)
>DroSec_CAF1 68458 98 - 1
CGCAGCGGUUCCGAGAUCGAAUUGUCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGGGUCCAGGUCGCUGUCGGCACCGGCUGAGAA
..(((((((.((((.(.(((.(((....(((((((((.((((((.(.....).)))))).)))))))))..))).))).).)))).))).)))).... ( -45.80)
>DroSim_CAF1 70564 98 - 1
CGCAGCGGUUCCGAGAUCGAAUUGUCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGGGUCCAGGUCGCUGUCGGCACCGGCUGAGAA
..(((((((.((((.(.(((.(((....(((((((((.((((((.(.....).)))))).)))))))))..))).))).).)))).))).)))).... ( -45.80)
>DroEre_CAF1 68847 98 - 1
CGCAGCGGCUCCGAGAUCGAGUUGUCCUCCUCCUCAAACUCCUGCACGAACUGCAGCGGAUUGAGAGCGUCCAGAUCGCUGUCGGCACCGGCUGCGAA
((((((((..((((.(.(((.(((..(..(((.((((.((.(((((.....))))).)).))))))).)..))).))).).))))..)).)))))).. ( -40.10)
>DroYak_CAF1 79521 98 - 1
CGCAGCGGUUCCGAGAUCGAGUUGUCCUCCUCCUCAAACUCCUGAACGAACUGCAGGGGAUUGAGUGCGUCCAGAUCGCUAUCGGCACCGGCUGGGAA
(.(((((((.((((...(((.(((..(.(...(((((.((((((.........)))))).))))).).)..))).)))...)))).))).)))).).. ( -36.40)
>DroAna_CAF1 69591 87 - 1
UGGGGCAGGUCCAGGGCGGAGGAGUCGCUCUCUU---UCUCCUCCACGUAUUGGAUGGGAUCCAGAGGGUCCAUUUCGCUGAUGGCU------AA--A
...(((..((((((.(.(((((((..........---.))))))).)...)))))).((((((...)))))).....))).......------..--. ( -30.40)
>consensus
CGCAGCGGUUCCGAGAUCGAGUUGUCCUCCUCCUCGAACUCCUGGACAAACUGCAGGGGAUUGAGGGCGUCCAGAUCGCUGUCGGCACCGGCUGAGAA
..(((((((.((((.(.(((.(((.....(((.((((.((((((.........)))))).)))))))....))).))).).)))).))).)))).... (-23.49 = -24.97 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:57 2006