Locus 1030

Sequence ID	2R_DroMel_CAF1
Location	4,239,616 – 4,239,706
Length	90
Max. P	0.728495

overview

Window 9

Location	4,239,616 – 4,239,706
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	82.33
Mean single sequence MFE	-19.25
Consensus MFE	-16.54
Energy contribution	-16.43
Covariance contribution	-0.11
Combinations/Pair	1.08
Mean z-score	-1.22
Structure conservation index	0.86
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4239616 90 + 20766785
AUUAUAUCAUUAAAAACUAAAAUCCUUUUAUUCUGCAUUCACAGUAGUCCUCAGCAGCUGGACGAUGAGCAGUUCUUUGAGAACUGCAUG
......(((((.....................(((......)))..((((.........)))))))))(((((((.....)))))))... ( -20.50)
>DroSec_CAF1 1164 88 + 1
AUUAUGUCAUAAAAAACUUUAAUUCUUU--UUCUACAUUUGCAGUAGUCCUCAGCAGCUGGACGAUGAGCAGUUCUUUGAGAACUGCAUG
......((((..................--...(((.......)))((((.........)))).))))(((((((.....)))))))... ( -18.10)
>DroSim_CAF1 2669 87 + 1
AUUAUGUCAUAAA-AACUAAAAUCACUU--UUCUACAUUUACAGUAGUCCUCAGCAGCUGGACGAUGAGCAGUUCUUUGAGAACUGCAUG
......((((...-..............--...(((.......)))((((.........)))).))))(((((((.....)))))))... ( -18.10)
>DroEre_CAF1 1177 90 + 1
AUUAUGGCAGUAAAAACCAAAAUUCUUUUAUUCUGCCUUUACAGUAGUCCUCAGCAGCUGGACGAUGAGCAGUUCUUUGAGAACUGCAUG
.....((((((((((..........)))))..)))))....((...((((.........))))..)).(((((((.....)))))))... ( -24.30)
>DroYak_CAF1 1167 90 + 1
AUGAUGUCAGUUAAAACUAAAAUCUUUUUGUUCUGCCUUUACAGUAGUCCUCAGCAGCUGGACGAUGAGCAGUUUUUUGAAAACUGCAUG
...(((.(((((((((((...(((........(((......)))..((((.........)))))))....)))))).....)))))))). ( -16.10)
>DroAna_CAF1 1177 78 + 1
ACUAUAGCAUUA----------UC--UUUCUUCCGAAAUUACAGCAGUCCGACGCAGCUGGACGACGAGCAGUUCUUUGAGAACUGCAUG
......((....----------..--((((....)))).....)).(((((.......))))).....(((((((.....)))))))... ( -18.40)
>consensus
AUUAUGUCAUUAAAAACUAAAAUCCUUUU_UUCUGCAUUUACAGUAGUCCUCAGCAGCUGGACGAUGAGCAGUUCUUUGAGAACUGCAUG
.........................................((...((((.........))))..)).(((((((.....)))))))... (-16.54 = -16.43 +  -0.11)

alignment

secondary structure

dotplot

Window 0

Location	4,239,616 – 4,239,706
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	82.33
Mean single sequence MFE	-20.67
Consensus MFE	-16.81
Energy contribution	-16.23
Covariance contribution	-0.58
Combinations/Pair	1.27
Mean z-score	-1.64
Structure conservation index	0.81
SVM decision value	0.42
SVM RNA-class probability	0.728495
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4239616 90 - 20766785
CAUGCAGUUCUCAAAGAACUGCUCAUCGUCCAGCUGCUGAGGACUACUGUGAAUGCAGAAUAAAAGGAUUUUAGUUUUUAAUGAUAUAAU
...(((((((.....)))))))((((.((((.........))))..((((....))))......................))))...... ( -19.40)
>DroSec_CAF1 1164 88 - 1
CAUGCAGUUCUCAAAGAACUGCUCAUCGUCCAGCUGCUGAGGACUACUGCAAAUGUAGAA--AAAGAAUUAAAGUUUUUUAUGACAUAAU
...(((((((.....)))))))((((.((((.........))))..((((....))))..--(((((((....)))))))))))...... ( -20.30)
>DroSim_CAF1 2669 87 - 1
CAUGCAGUUCUCAAAGAACUGCUCAUCGUCCAGCUGCUGAGGACUACUGUAAAUGUAGAA--AAGUGAUUUUAGUU-UUUAUGACAUAAU
...(((((((.....))))))).....(((.....(((((((..((((............--.)))).))))))).-.....)))..... ( -18.12)
>DroEre_CAF1 1177 90 - 1
CAUGCAGUUCUCAAAGAACUGCUCAUCGUCCAGCUGCUGAGGACUACUGUAAAGGCAGAAUAAAAGAAUUUUGGUUUUUACUGCCAUAAU
...(((((((.....))))))).....((((.........)))).........(((((..((((((........)))))))))))..... ( -23.70)
>DroYak_CAF1 1167 90 - 1
CAUGCAGUUUUCAAAAAACUGCUCAUCGUCCAGCUGCUGAGGACUACUGUAAAGGCAGAACAAAAAGAUUUUAGUUUUAACUGACAUCAU
...(((((((.....))))))).....((((.........))))..((((....))))........(((.(((((....))))).))).. ( -20.30)
>DroAna_CAF1 1177 78 - 1
CAUGCAGUUCUCAAAGAACUGCUCGUCGUCCAGCUGCGUCGGACUGCUGUAAUUUCGGAAGAAA--GA----------UAAUGCUAUAGU
...(((((((.....)))))))(((.(((......))).)))((((..(((.((((....))))--..----------...)))..)))) ( -22.20)
>consensus
CAUGCAGUUCUCAAAGAACUGCUCAUCGUCCAGCUGCUGAGGACUACUGUAAAUGCAGAA_AAAAGGAUUUUAGUUUUUAAUGACAUAAU
...(((((((.....))))))).....((((.........))))..((((....))))................................ (-16.81 = -16.23 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:43 2006