Locus 1344

Sequence ID	X_DroMel_CAF1
Location	4,030,254 – 4,030,386
Length	132
Max. P	0.998598

overview

Window 4

Location	4,030,254 – 4,030,350
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	94.90
Mean single sequence MFE	-29.36
Consensus MFE	-26.06
Energy contribution	-26.10
Covariance contribution	0.04
Combinations/Pair	1.11
Mean z-score	-2.30
Structure conservation index	0.89
SVM decision value	3.15
SVM RNA-class probability	0.998598
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4030254 96 - 22224390
UUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACGUUGGGAUCUGCUAACUUCUUCUUCUGCCUUCCUGUUAUGUUUCACUAUUUUUC
.(((((((((((((((((.(....).)))))))))..)))..(((((......)))))..............)))))................... ( -29.20)
>DroSec_CAF1 44013 93 - 1
UUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUAACUUC---UUCUGCCUUCCUGUUAUGUUCCACUAUUUUUC
.(((((((((((((((((.(....).)))))))))..)))((((.((((...((.......---....))..))))...)))).)).)))...... ( -30.90)
>DroSim_CAF1 40250 93 - 1
UUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUAACUUC---UUCUGCCUUCCUGUUAUGUUCCACUAUUUUUC
.(((((((((((((((((.(....).)))))))))..)))((((.((((...((.......---....))..))))...)))).)).)))...... ( -30.90)
>DroEre_CAF1 43757 93 - 1
UUAGGGGCGUGUCAGCCCCGGCAACAGUGUUGCUAACCGCACAUUGGGAUCUGCUGACUUC---UUCUGCCUUCCUGUUAUGUUUCACUAUUUUUC
...(((((......)))))((((.((((((.((.....))))))))(((((....)).)))---...))))......................... ( -25.90)
>DroYak_CAF1 42447 93 - 1
UAAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUGACUUC---UUCUGCCUUCCUGUUAUGUUUCACUACUUUUC
.(((((((((((((((((.(....).)))))))))..)))((((.((((...((.((....---.)).))..))))...)))).......))))). ( -29.90)
>consensus
UUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUAACUUC___UUCUGCCUUCCUGUUAUGUUUCACUAUUUUUC
.(((((((((((((((((.(....).)))))))))..)))((((.((((...((..............))..))))...)))).)).)))...... (-26.06 = -26.10 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	4,030,278 – 4,030,386
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	94.92
Mean single sequence MFE	-36.40
Consensus MFE	-32.70
Energy contribution	-33.26
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.53
Structure conservation index	0.90
SVM decision value	1.32
SVM RNA-class probability	0.941590
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4030278 108 - 22224390
AAAACAGCAACAAUGUGUCUGGGUCGUGAAGGCAUUUUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACGUUGGGAUCUGCUAACUUCUUCUUCUGCCU
.....((((.((((((((....(((.....))).......((...(((((((((.(....).))))))))).)))))))))).....))))................. ( -35.70)
>DroSec_CAF1 44037 105 - 1
AAAACAGCAACAAUGUGUCUGGGACGUGAAGGCAUUUUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUAACUUC---UUCUGCCU
.....((((.((((((((((((((.((....)).))))))((...(((((((((.(....).))))))))).)))))))))).....))))......---........ ( -36.70)
>DroSim_CAF1 40274 105 - 1
AAAACAGCAACAAUGUGUCUGGGACGUGAAGGCAUUUUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUAACUUC---UUCUGCCU
.....((((.((((((((((((((.((....)).))))))((...(((((((((.(....).))))))))).)))))))))).....))))......---........ ( -36.70)
>DroEre_CAF1 43781 105 - 1
AAAGCAGCUACAAUGUGUCUAGGACGUGAAGGCAUUUUAGGGGCGUGUCAGCCCCGGCAACAGUGUUGCUAACCGCACAUUGGGAUCUGCUGACUUC---UUCUGCCU
..(((((...((((((((...((................(((((......)))))((((((...))))))..))))))))))....)))))......---........ ( -35.70)
>DroYak_CAF1 42471 105 - 1
AAAACAGCAACAAUGUGUCUGGGACGUGAAGGCAUUUAAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUGACUUC---UUCUGCCU
....(((((.((((((((((..((.((....)).))..))((...(((((((((.(....).))))))))).)))))))))).....))))).....---........ ( -37.20)
>consensus
AAAACAGCAACAAUGUGUCUGGGACGUGAAGGCAUUUUAGGGGCGUGGCAGCACCGGCAACAGUGUUGCCAACCGCACAUUGGGAUCUGCUAACUUC___UUCUGCCU
.....((((.((((((((((((((.((....)).))))))((...(((((((((.(....).))))))))).)))))))))).....))))................. (-32.70 = -33.26 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:02 2006