Locus 1829

Sequence ID	3R_DroMel_CAF1
Location	5,234,225 – 5,234,320
Length	95
Max. P	0.916329

overview

Window 8

Location	5,234,225 – 5,234,320
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-28.94
Consensus MFE	-17.14
Energy contribution	-20.30
Covariance contribution	3.16
Combinations/Pair	1.16
Mean z-score	-2.42
Structure conservation index	0.59
SVM decision value	1.11
SVM RNA-class probability	0.916329
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5234225 95 + 27905053
GAAUCCAUAUAGGAAAUAUGUACAACCGACGGGCCUCGAAGCACAAUAUGCUAAGGCCCAAAGAUCCAAUGUGUUGUGCCUUCCUAAUGGGUUCC
((((((((.((((((....(((((((((..((((((...((((.....)))).))))))...(...)..)).))))))).)))))))))))))). ( -36.00)
>DroSec_CAF1 7987 95 + 1
GAUUCCAAAUAGGAAAUAUGUACAAUCGACGGGCCUCGAAGCACAAUAUGCUGAGGCCCAAGGAUCCAGUGUAUUGUUCCUUCCUCAAGGGUUCC
((..((....(((((....(((((......(((((((..((((.....)))))))))))..(....)..)))))..))))).......))..)). ( -29.10)
>DroSim_CAF1 8047 95 + 1
GAUUCCUAAUAGGAAAUAUGUACAAUCGACGGGCCUCGAAGCACAAUAUGCUGAGGCCCAGAGAUCCAGUGUAAUGUUCCUUCCUCAUGGGUUCC
((..((((..(((((((((.(((((((...(((((((..((((.....)))))))))))...)))....))))))))...)))))..)))).)). ( -29.80)
>DroEre_CAF1 10233 92 + 1
AAAUCCAAAUAGGAAAUAUGUACUACCGACGGGACUCGAAGGCCAG--UGCUGAGACCCGUAGAACCAGUGCAUUGUGC-UCCUUAAUGUGUUUC
(((..((...((((.(((((((((....(((((.(((...(((...--.)))))).)))))......)))))).)))..-))))...))..))). ( -24.70)
>DroYak_CAF1 7996 92 + 1
AAAUCCAAAUAGGAAAUAUGUACAAUCGACGGGCCUUGAGGGACAU--UGUUCAGGCCCAAAGAUCCAGUCUAUUGUGC-UCCUUAAUCGGUUCU
.((((.....((((.....(((((((.(((((((((.(((.(....--).)))))))))...(...).))).)))))))-)))).....)))).. ( -25.10)
>consensus
GAAUCCAAAUAGGAAAUAUGUACAAUCGACGGGCCUCGAAGCACAAUAUGCUGAGGCCCAAAGAUCCAGUGUAUUGUGCCUUCCUAAUGGGUUCC
((((((...((((((....(((((((..(((((((((..((((.....))))))))))).........))..))))))).))))))..)))))). (-17.14 = -20.30 +   3.16)

alignment

secondary structure

dotplot

Window 9

Location	5,234,225 – 5,234,320
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	81.52
Mean single sequence MFE	-27.76
Consensus MFE	-18.18
Energy contribution	-20.22
Covariance contribution	2.04
Combinations/Pair	1.15
Mean z-score	-1.75
Structure conservation index	0.65
SVM decision value	0.19
SVM RNA-class probability	0.628467
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5234225 95 - 27905053
GGAACCCAUUAGGAAGGCACAACACAUUGGAUCUUUGGGCCUUAGCAUAUUGUGCUUCGAGGCCCGUCGGUUGUACAUAUUUCCUAUAUGGAUUC
.(((.(((((((((((...(((....)))((((..(((((((((((((...)))))..))))))))..)))).......))))))).)))).))) ( -32.60)
>DroSec_CAF1 7987 95 - 1
GGAACCCUUGAGGAAGGAACAAUACACUGGAUCCUUGGGCCUCAGCAUAUUGUGCUUCGAGGCCCGUCGAUUGUACAUAUUUCCUAUUUGGAAUC
.....((...((((((......((((....(((..(((((((((((((...)))))..))))))))..)))))))....))))))....)).... ( -30.70)
>DroSim_CAF1 8047 95 - 1
GGAACCCAUGAGGAAGGAACAUUACACUGGAUCUCUGGGCCUCAGCAUAUUGUGCUUCGAGGCCCGUCGAUUGUACAUAUUUCCUAUUAGGAAUC
....((....((((((......((((.(.(((....((((((((((((...)))))..)))))))))).).))))....))))))....)).... ( -30.40)
>DroEre_CAF1 10233 92 - 1
GAAACACAUUAAGGA-GCACAAUGCACUGGUUCUACGGGUCUCAGCA--CUGGCCUUCGAGUCCCGUCGGUAGUACAUAUUUCCUAUUUGGAUUU
......((...((((-(....(((.((((..((.(((((.(((.((.--...))....))).))))).)))))).)))..)))))...))..... ( -21.50)
>DroYak_CAF1 7996 92 - 1
AGAACCGAUUAAGGA-GCACAAUAGACUGGAUCUUUGGGCCUGAACA--AUGUCCCUCAAGGCCCGUCGAUUGUACAUAUUUCCUAUUUGGAUUU
....((((...((((-....((((.....((((..(((((((((...--.......)).)))))))..)))).....))))))))..)))).... ( -23.60)
>consensus
GGAACCCAUUAGGAAGGCACAAUACACUGGAUCUUUGGGCCUCAGCAUAUUGUGCUUCGAGGCCCGUCGAUUGUACAUAUUUCCUAUUUGGAUUC
....((...((((((....((......))((((..((((((((((((.....))))..))))))))..))))........))))))...)).... (-18.18 = -20.22 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:31 2006