Locus 230

Sequence ID	3L_DroMel_CAF1
Location	630,139 – 630,237
Length	98
Max. P	0.652348

overview

Window 0

Location	630,139 – 630,237
Length	98
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-31.96
Consensus MFE	-20.36
Energy contribution	-20.36
Covariance contribution	-0.00
Combinations/Pair	1.21
Mean z-score	-1.65
Structure conservation index	0.64
SVM decision value	-0.04
SVM RNA-class probability	0.514864
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 630139 98 + 23771897
---AAAACGUCACGAAAU-------AUGUAUAAAUUGCUUAAUUUGUGAUAAGCAUUUAUGGUGGCCCGGGCGAUCCCAGUUUCCAAGUCGGUCUCCGU------UG------GGCCAUG
---.....((((((((.(-------(.(((.....))).)).))))))))...........((((((((((....)))...........(((...))).------.)------)))))). ( -28.40)
>DroSec_CAF1 41571 108 + 1
--GAAAACGUCACGAAAUACA---UAUGUAUAAAUUGCUUAAUUUGUGAUAAGCAUUUAUGGUGGCCCGGGCGAUCCCAGU-UCCAAGUCGGUCUCCGU------CGGAUCAGGGUCAUG
--...................---....(((((((.(((((........))))))))))))((((((((((....))).(.-(((..(.(((...))).------)))).).))))))). ( -27.50)
>DroSim_CAF1 39822 104 + 1
--GAAAACGUCACGAAAU-------AUGUAUAAAUUGCUUAAUUUGUGAUAAGCAUUUAUGGUGGCCCGGGCGAUCCCAGU-UCCAAGUCGGUCUCCGU------CGGAUCAGGGCCAUG
--......((((((((.(-------(.(((.....))).)).))))))))...........((((((((((....))).(.-(((..(.(((...))).------)))).).))))))). ( -32.40)
>DroYak_CAF1 46271 113 + 1
CGAAAAACGCCAUGAAAUAUGUACUAUGUAUAAAUUGCUUAAUUUGUGAUAAGCAUUUAUGGUGGCCCAGGCGAUCCCAGU-GCCAAGUCGCUCUUCGU------CGGCUCAGGGCCAUG
........((((((((...(((((...)))))...((((((........))))))))))))))(((((.((((.......)-))).((((((.....).------)))))..)))))... ( -34.80)
>DroAna_CAF1 51582 103 + 1
---AAAAUGCCACGAAAU-----------GUAAAUUGCUUAAUUUGUGAUAAACAUUUAUGGUGGCCCAGGCGG---CAGAGUCGGAGUCGGUCUCCGAGUCGAACGGAUCAGGGCCAUG
---.....((((..((((-----------((..((..(.......)..))..)))))).))))(((((.((((.---..((.((((((.....)))))).))...))..)).)))))... ( -36.70)
>consensus
___AAAACGUCACGAAAU_______AUGUAUAAAUUGCUUAAUUUGUGAUAAGCAUUUAUGGUGGCCCGGGCGAUCCCAGU_UCCAAGUCGGUCUCCGU______CGGAUCAGGGCCAUG
............................(((((((.(((((........))))))))))))((((((((((((((............)))).)))(((.......)))....))))))). (-20.36 = -20.36 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	630,139 – 630,237
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.40
Mean single sequence MFE	-28.76
Consensus MFE	-19.00
Energy contribution	-19.28
Covariance contribution	0.28
Combinations/Pair	1.17
Mean z-score	-1.76
Structure conservation index	0.66
SVM decision value	0.25
SVM RNA-class probability	0.652348
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 630139 98 - 23771897
CAUGGCC------CA------ACGGAGACCGACUUGGAAACUGGGAUCGCCCGGGCCACCAUAAAUGCUUAUCACAAAUUAAGCAAUUUAUACAU-------AUUUCGUGACGUUUU---
..(((((------(.------.(((...)))....(....).(((....)))))))))..(((((((((((........))))).))))))....-------...............--- ( -26.60)
>DroSec_CAF1 41571 108 - 1
CAUGACCCUGAUCCG------ACGGAGACCGACUUGGA-ACUGGGAUCGCCCGGGCCACCAUAAAUGCUUAUCACAAAUUAAGCAAUUUAUACAUA---UGUAUUUCGUGACGUUUUC--
((((((((...((((------((((...)))..)))))-...(((....)))))).....(((((((((((........))))).)))))).....---......)))))........-- ( -25.40)
>DroSim_CAF1 39822 104 - 1
CAUGGCCCUGAUCCG------ACGGAGACCGACUUGGA-ACUGGGAUCGCCCGGGCCACCAUAAAUGCUUAUCACAAAUUAAGCAAUUUAUACAU-------AUUUCGUGACGUUUUC--
..((((((...((((------((((...)))..)))))-...(((....)))))))))..(((((((((((........))))).))))))....-------................-- ( -29.60)
>DroYak_CAF1 46271 113 - 1
CAUGGCCCUGAGCCG------ACGAAGAGCGACUUGGC-ACUGGGAUCGCCUGGGCCACCAUAAAUGCUUAUCACAAAUUAAGCAAUUUAUACAUAGUACAUAUUUCAUGGCGUUUUUCG
..((((.....))))------.(((((((((.((((((-.(..((....))..)))))..(((((((((((........))))).))))))..................))))))))))) ( -33.60)
>DroAna_CAF1 51582 103 - 1
CAUGGCCCUGAUCCGUUCGACUCGGAGACCGACUCCGACUCUG---CCGCCUGGGCCACCAUAAAUGUUUAUCACAAAUUAAGCAAUUUAC-----------AUUUCGUGGCAUUUU---
..((((((.....((...((.((((((.....)))))).))..---.))...))))))((((((((((..((..(.......)..))..))-----------)))).))))......--- ( -28.60)
>consensus
CAUGGCCCUGAUCCG______ACGGAGACCGACUUGGA_ACUGGGAUCGCCCGGGCCACCAUAAAUGCUUAUCACAAAUUAAGCAAUUUAUACAU_______AUUUCGUGACGUUUU___
..((((((..............(.(((.....))).).....(((....)))))))))..(((((((((((........))))).))))))............................. (-19.00 = -19.28 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:54 2006