Locus 5420

Sequence ID	2L_DroMel_CAF1
Location	15,454,626 – 15,454,717
Length	91
Max. P	0.955063

overview

Window 5

Location	15,454,626 – 15,454,717
Length	91
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	88.20
Mean single sequence MFE	-43.66
Consensus MFE	-28.66
Energy contribution	-29.46
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.66
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15454626 91 + 22407834
UUGGCCACACAGGGCGAGCAGGGGCCAGUUGAGCGGUGCCCAGU--------UGCCCAGUUGGCCACUUGGCAACUCGGCCUG-CCGAGAGAUGUGUGCU
..(((((((((((.(((((((((((((..((.((..(.....).--------.)).))..))))).))))....)))).))))-.(....).)))).))) ( -39.10)
>DroSec_CAF1 192678 81 + 1
UUGGCCACACAGGGCGAGCAGGGGCCAGUUGAGCGGUGCCC----------------AGUUGGCCACUUGGCAACUCGUCCUG-CCGA--GAUGUGUGCU
..(((((((((((((((((((((((((..((.((...)).)----------------)..))))).))))....)))))))))-....--..)))).))) ( -37.00)
>DroSim_CAF1 198610 89 + 1
UUGGCCACACAGGGCGUGCAGGGGCCAGUUGAGCGGUGCCCAGU--------UGCCCAGUUGGCCACUUGGCAACUCGGCCUG-CCGA--GAUGUGUGCU
.((((((.((.(((((.((.((((((........))).))).))--------))))).))))))))....(((.(((((....-))))--).)))..... ( -39.20)
>DroEre_CAF1 202936 97 + 1
UUGGCCACACAGGGCGAGCAGGGGCCAGUUGAGCGGUGCCCAGUUGCCCAGUUGCCCAGUUGGCCACUUGGCAACUGGGCCUG-CCGA--GAUGUGUGGU
...((((((((.(((........)))..(((.((((.(((((((((((.(((.(((.....))).))).))))))))))))))-))))--..)))))))) ( -56.00)
>DroYak_CAF1 200222 98 + 1
UUGGCCACACAGGGCGAGCAGGGGCCAGUUGAGCGGUACCCAGUUGCCGAGUUGCCCAGUUGGCCACUUGGCAACUCGGCCUGGCCGA--GAUGUGUGCU
..(((.(((((.(((.((..((((((........))).)))....(((((((((((.(((.....))).))))))))))))).)))..--..)))))))) ( -47.00)
>consensus
UUGGCCACACAGGGCGAGCAGGGGCCAGUUGAGCGGUGCCCAGU________UGCCCAGUUGGCCACUUGGCAACUCGGCCUG_CCGA__GAUGUGUGCU
.....((((((...((.((((((((..(.....)...))))............(((.(((((.((....))))))).)))))).))).....)))))).. (-28.66 = -29.46 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	15,454,626 – 15,454,717
Length	91
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	88.20
Mean single sequence MFE	-41.88
Consensus MFE	-29.50
Energy contribution	-30.14
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-3.12
Structure conservation index	0.70
SVM decision value	1.45
SVM RNA-class probability	0.955063
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15454626 91 - 22407834
AGCACACAUCUCUCGG-CAGGCCGAGUUGCCAAGUGGCCAACUGGGCA--------ACUGGGCACCGCUCAACUGGCCCCUGCUCGCCCUGUGUGGCCAA
.((.(((((....(((-((((((.(((((((.(((.....))).))))--------))).)))...(((.....)))..)))).))....)))))))... ( -38.60)
>DroSec_CAF1 192678 81 - 1
AGCACACAUC--UCGG-CAGGACGAGUUGCCAAGUGGCCAACU----------------GGGCACCGCUCAACUGGCCCCUGCUCGCCCUGUGUGGCCAA
..((((((..--.(((-((((.(.(((((....(((.((....----------------)).)))....))))).)..))))).))...))))))..... ( -32.50)
>DroSim_CAF1 198610 89 - 1
AGCACACAUC--UCGG-CAGGCCGAGUUGCCAAGUGGCCAACUGGGCA--------ACUGGGCACCGCUCAACUGGCCCCUGCACGCCCUGUGUGGCCAA
..((((((..--.(((-((((((.(((((((.(((.....))).))))--------))).)))...(((.....)))..)))).))...))))))..... ( -39.40)
>DroEre_CAF1 202936 97 - 1
ACCACACAUC--UCGG-CAGGCCCAGUUGCCAAGUGGCCAACUGGGCAACUGGGCAACUGGGCACCGCUCAACUGGCCCCUGCUCGCCCUGUGUGGCCAA
.(((((((..--.(((-((((((((((((((.(((.(((.....))).))).)))))))))))...(((.....)))..)))).))...))))))).... ( -52.10)
>DroYak_CAF1 200222 98 - 1
AGCACACAUC--UCGGCCAGGCCGAGUUGCCAAGUGGCCAACUGGGCAACUCGGCAACUGGGUACCGCUCAACUGGCCCCUGCUCGCCCUGUGUGGCCAA
..((((((..--..(((((((((((((((((.(((.....))).)))))))))))...((((.....)))).))))))...(....)..))))))..... ( -46.80)
>consensus
AGCACACAUC__UCGG_CAGGCCGAGUUGCCAAGUGGCCAACUGGGCA________ACUGGGCACCGCUCAACUGGCCCCUGCUCGCCCUGUGUGGCCAA
..((((((.....(((.((((((.(((((((....)).))))).)))............((((............))))))).)))...))))))..... (-29.50 = -30.14 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:44 2006