Locus 398

Sequence ID	3L_DroMel_CAF1
Location	1,173,535 – 1,173,631
Length	96
Max. P	0.536561

overview

Window 3

Location	1,173,535 – 1,173,631
Length	96
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.82
Mean single sequence MFE	-35.33
Consensus MFE	-22.06
Energy contribution	-22.57
Covariance contribution	0.50
Combinations/Pair	1.25
Mean z-score	-1.54
Structure conservation index	0.62
SVM decision value	0.01
SVM RNA-class probability	0.536561
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1173535 96 + 23771897
GAUCACAGGUACUUGACC---UCCGGAGGCAAUAGUCCCGGCUCCCGAUCCCGCACCCACUCUCGACAGAAUUCCGGAAGUGGAUCCGGAUCGGAGGAA
......((((.....)))---)((((.(((....)))))))(..(((((((.(...(((((..((.........))..)))))..).)))))))..).. ( -34.80)
>DroSec_CAF1 57379 96 + 1
GAUCAGAAGUACUUGACC---UCCGGAGGCAAUAGCCCCGGCUCCCGAUCCCGCACCCACUCUCGACAGAAUUCCGGAAGCGGGUCCGGAUCGGAGGAA
..((((......))))((---(((((.(((....)))))))...(((((((.(.((((.((..((.........))..)).))))).)))))))))).. ( -38.90)
>DroSim_CAF1 55877 96 + 1
GAUCAGAAGUACUUGACC---UCCGGAGGCAAUAGCCCCGGCUCCCGAUCCCGCACCCACUCUCGACAGAAUUCCGGAAGCGGGUCCGGGUCGGAGGAA
..((((......))))((---(((((.(((....)))))))...((((.((((.((((.((..((.........))..)).)))).))))))))))).. ( -40.20)
>DroEre_CAF1 55687 88 + 1
--------GUGCCUGACA---UCCGGGGGCAACAGCCCCGGCUCCCGAUCCCGCACCCACUCUCGCCAAAACUCCGGAAGCGCAUCCGCAUCGGAGGAA
--------((((..((..---..(((((((..........))))))).))..))))...............((((((..(((....))).))))))... ( -27.50)
>DroYak_CAF1 59758 96 + 1
GAGCACAAGUACCUGACC---UCCGGAGGCAACAGCCCCGGCUCCCGAUCCCGCACCCACUCUCGCCAAAACUCCGGCAGCGCAUCCGGAUCGGAGGAA
...........(((....---.((((.(((....)))))))...((((((((((..........(((........))).))).....)))))))))).. ( -29.70)
>DroAna_CAF1 62225 99 + 1
GACCAGCGCUCCUCGGGCGGAUCCAGAAGCAACAGCCCCGGCUUCCGGUCCCGCACCCACUCCCGCUCCAGUUCGGGCUUCGGUUCCGGAUUGGAAGAC
.....(((......((((((..((.(((((..........))))).))..)))).))......)))((((((((((((....).))))))))))).... ( -40.90)
>consensus
GAUCAGAAGUACUUGACC___UCCGGAGGCAACAGCCCCGGCUCCCGAUCCCGCACCCACUCUCGACAGAAUUCCGGAAGCGGAUCCGGAUCGGAGGAA
......................((((.(((....)))))))((.(((((((.(...((.((.(((.........))).)).))..).))))))).)).. (-22.06 = -22.57 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	1,173,535 – 1,173,631
Length	96
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	80.82
Mean single sequence MFE	-41.23
Consensus MFE	-31.52
Energy contribution	-32.33
Covariance contribution	0.81
Combinations/Pair	1.24
Mean z-score	-1.13
Structure conservation index	0.76
SVM decision value	0.00
SVM RNA-class probability	0.534992
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1173535 96 - 23771897
UUCCUCCGAUCCGGAUCCACUUCCGGAAUUCUGUCGAGAGUGGGUGCGGGAUCGGGAGCCGGGACUAUUGCCUCCGGA---GGUCAAGUACCUGUGAUC
..(..(((((((.((((((((..(((.......)))..))))))).).)))))))..).(((((((...((((....)---)))..))).))))..... ( -39.20)
>DroSec_CAF1 57379 96 - 1
UUCCUCCGAUCCGGACCCGCUUCCGGAAUUCUGUCGAGAGUGGGUGCGGGAUCGGGAGCCGGGGCUAUUGCCUCCGGA---GGUCAAGUACUUCUGAUC
..(..(((((((.((((((((..(((.......)))..))))))).).)))))))..)(((((((....))).)))).---(((((........))))) ( -46.40)
>DroSim_CAF1 55877 96 - 1
UUCCUCCGACCCGGACCCGCUUCCGGAAUUCUGUCGAGAGUGGGUGCGGGAUCGGGAGCCGGGGCUAUUGCCUCCGGA---GGUCAAGUACUUCUGAUC
..(..((((((((.(((((((..(((.......)))..))))))).)))).))))..)(((((((....))).)))).---(((((........))))) ( -48.00)
>DroEre_CAF1 55687 88 - 1
UUCCUCCGAUGCGGAUGCGCUUCCGGAGUUUUGGCGAGAGUGGGUGCGGGAUCGGGAGCCGGGGCUGUUGCCCCCGGA---UGUCAGGCAC--------
....((((((.(.(((.((((..((.........))..)))).)).).).)))))).((((((((....)))))..(.---...).)))..-------- ( -33.80)
>DroYak_CAF1 59758 96 - 1
UUCCUCCGAUCCGGAUGCGCUGCCGGAGUUUUGGCGAGAGUGGGUGCGGGAUCGGGAGCCGGGGCUGUUGCCUCCGGA---GGUCAGGUACUUGUGCUC
..((((((((((.(((.(((((((((....)))))...)))).)).).)))))))...(((((((....))).)))))---))...((((....)))). ( -40.10)
>DroAna_CAF1 62225 99 - 1
GUCUUCCAAUCCGGAACCGAAGCCCGAACUGGAGCGGGAGUGGGUGCGGGACCGGAAGCCGGGGCUGUUGCUUCUGGAUCCGCCCGAGGAGCGCUGGUC
((.((((....(((.(((.(..((((........))))..).)))(((((.((((((((..........)))))))).)))))))).)))).))..... ( -39.90)
>consensus
UUCCUCCGAUCCGGAUCCGCUUCCGGAAUUCUGGCGAGAGUGGGUGCGGGAUCGGGAGCCGGGGCUAUUGCCUCCGGA___GGUCAAGUACUUCUGAUC
....(((((((((.(((((((..((.........))..))))))).)))).)))))..(((((((....))).))))...................... (-31.52 = -32.33 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:54 2006