Locus 1957

Sequence ID	3L_DroMel_CAF1
Location	5,414,702 – 5,414,812
Length	110
Max. P	0.931604

overview

Window 2

Location	5,414,702 – 5,414,812
Length	110
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	94.19
Mean single sequence MFE	-39.84
Consensus MFE	-28.72
Energy contribution	-28.76
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-3.29
Structure conservation index	0.72
SVM decision value	0.70
SVM RNA-class probability	0.826154
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5414702 110 + 23771897
ACAGUUAACAUGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGACUGAGUGAGAAGGAUUCCGGAUC-CAGGAAGCAGAAACCAG-------GAUCCAUGGCCAAUC
....................(((((((((.(((((..((..((.....))..))..)))))............(((((-(.((.........)).)-------)))))))))))))). ( -34.20)
>DroSec_CAF1 10288 111 + 1
ACAGUUAACAUGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUUCCGGAUCCCAGGAAGCAGGAACCAG-------GAUCCAUGGCCAAUC
....................(((((((((.((((((.((..((.....))..)).)))))).....((((((.((.(((..(....).))).)).)-------)))))))))))))). ( -38.70)
>DroSim_CAF1 11479 111 + 1
ACAGUUAACAUGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUUCCGGAUCCCAGGAAGCAGGAACCAG-------GAUCCAUGGCCAAUC
....................(((((((((.((((((.((..((.....))..)).)))))).....((((((.((.(((..(....).))).)).)-------)))))))))))))). ( -38.70)
>DroEre_CAF1 10192 110 + 1
ACAGUUAACAUGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUCCAGGAUC-CAGGAAGCAGGAACCAG-------GAUCCAUGGCCAAUC
....................(((((((((.((((((.((..((.....))..)).)))))).....((((((.((.((-(.(....).))).)).)-------)))))))))))))). ( -41.90)
>DroYak_CAF1 9844 117 + 1
ACAGUUAACAUGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACUGAGGAGUGAGUGAGAAGGAUCCAGGAUC-CAGGAACCAGGAACCAGGAUUCAGGAUCCAUGGCCAAUC
....................(((((((((.((((((.(((((......))).)).)))))).....((((((.(((((-(.((.........)).)))))).))))))))))))))). ( -45.70)
>consensus
ACAGUUAACAUGUCCAAUUUAUUGGCCAUAACUCAUGCCCGGGAUCGACCAAGGAGUGAGUGAGAAGGAUUCCGGAUC_CAGGAAGCAGGAACCAG_______GAUCCAUGGCCAAUC
....................(((((((((.((((((.((..((.....))..)).))))))............(((((...(....).(....).........)))))))))))))). (-28.72 = -28.76 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	5,414,702 – 5,414,812
Length	110
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	94.19
Mean single sequence MFE	-39.04
Consensus MFE	-29.68
Energy contribution	-30.52
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-2.76
Structure conservation index	0.76
SVM decision value	1.21
SVM RNA-class probability	0.931604
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5414702 110 - 23771897
GAUUGGCCAUGGAUC-------CUGGUUUCUGCUUCCUG-GAUCCGGAAUCCUUCUCACUCAGUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACAUGUUAACUGU
.((((((((((((((-------(.((.........)).)-)))))............(((((((((..((.....)).)))).))))).))))))))).................... ( -37.20)
>DroSec_CAF1 10288 111 - 1
GAUUGGCCAUGGAUC-------CUGGUUCCUGCUUCCUGGGAUCCGGAAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACAUGUUAACUGU
.(((((((((((((.-------((((.((((.......)))).)))).)))).....(((((..(((.((.....)).)))..))))).))))))))).................... ( -39.50)
>DroSim_CAF1 11479 111 - 1
GAUUGGCCAUGGAUC-------CUGGUUCCUGCUUCCUGGGAUCCGGAAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACAUGUUAACUGU
.(((((((((((((.-------((((.((((.......)))).)))).)))).....(((((..(((.((.....)).)))..))))).))))))))).................... ( -39.50)
>DroEre_CAF1 10192 110 - 1
GAUUGGCCAUGGAUC-------CUGGUUCCUGCUUCCUG-GAUCCUGGAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACAUGUUAACUGU
.((((((((((((((-------(.((.(((........)-)).)).)))))).....(((((..(((.((.....)).)))..))))).))))))))).................... ( -41.90)
>DroYak_CAF1 9844 117 - 1
GAUUGGCCAUGGAUCCUGAAUCCUGGUUCCUGGUUCCUG-GAUCCUGGAUCCUUCUCACUCACUCCUCAGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACAUGUUAACUGU
.(((((((((((((((.(.((((.((.........)).)-))).).)))))).....(((((..(((..(.....)..)))..))))).))))))))).................... ( -37.10)
>consensus
GAUUGGCCAUGGAUC_______CUGGUUCCUGCUUCCUG_GAUCCGGAAUCCUUCUCACUCACUCCUUGGUCGAUCCCGGGCAUGAGUUAUGGCCAAUAAAUUGGACAUGUUAACUGU
.((((((((((.............((.(((((..((....))..))))).)).....(((((..(((.((.....)).)))..))))))))))))))).................... (-29.68 = -30.52 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:03 2006