Locus 1416

Sequence ID	2R_DroMel_CAF1
Location	5,472,336 – 5,472,438
Length	102
Max. P	0.656075

overview

Window 4

Location	5,472,336 – 5,472,438
Length	102
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	81.45
Mean single sequence MFE	-29.45
Consensus MFE	-18.36
Energy contribution	-19.25
Covariance contribution	0.89
Combinations/Pair	1.17
Mean z-score	-1.87
Structure conservation index	0.62
SVM decision value	0.23
SVM RNA-class probability	0.643795
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5472336 102 + 20766785
AGACUCAAAGUCCACAGCGUUAUCUGCAUAAUGUGGACAGCAAU---AG---------CAACAACAACGAACGCCUGCACCAGAUACUCAAGGGAUCCGGAGCAGGAUCGGGAG
...(((...((((((((((.....)))....))))))).((...---.)---------)........(((...(((((.((.(((.((....))))).)).))))).))).))) ( -32.50)
>DroSec_CAF1 1 100 + 1
--ACUCAAAGUCCAUCGCGUUAUCUGCAUAAUGUGGACAGCAAU---AA---------UAACAACAACGAACGCCUGCACCAGAUACUCAAGGGAUCCGGAGCAGGAUCGGGAA
--........(((.(((((((((....)))))))))........---..---------.........(((...(((((.((.(((.((....))))).)).))))).)))))). ( -27.90)
>DroSim_CAF1 3 102 + 1
AGACUCAAAGUCCAUCGCGUUAUCUGCAUAAUGUGGACAGCAAU---AA---------UAACAACAACGAACGCCUGCACCAGAUACUCAAGGGAUCCGGAGCAGGAUCGGGAG
...(((...((((...(((((((....)))))))))))......---..---------.........(((...(((((.((.(((.((....))))).)).))))).))).))) ( -29.30)
>DroEre_CAF1 2 102 + 1
AGACUCAAAGUUCGCAGCGUUAUCUGCAUAAUGUGGACAACAGC---AG---------UAACAACAACGAACGCCUGCAGCAAAUUCUCAAAGGAUCUGGAGCAGGAUCGGGUG
..((((...(((((..(((((.((..(.....)..)).))).))---.(---------(....))..))))).(((((..((.((((.....)))).))..)))))...)))). ( -28.80)
>DroYak_CAF1 3 102 + 1
AGACUCAAAGUCCGCCGCGUUAUCUGCAGAAUGCGGACAACAAC---AG---------UAACAACAACGAACGCCUGCACCAGAUUCUCAAAGGAUCCGGGGCAGGAUCGGGUG
.(((.....)))((((..(((.(((((.....))))).)))...---..---------.........(((...(((((.((.(((((.....))))).)).))))).))))))) ( -35.30)
>DroPer_CAF1 306 108 + 1
AGAGUCAAAGUUCGCCGCGUUAUCUGCAAAACAUUGACAUCAGCAACAAUGCCAGCAUCAACAACAACGAGAGACUGCAGCAGAUCCUCAAAGGAGCCGGAGCCGGCU------
.(((((((.(((....(((.....)))..))).))))).)).(((....)))................(((.(((((...))).))))).....(((((....)))))------ ( -22.90)
>consensus
AGACUCAAAGUCCACCGCGUUAUCUGCAUAAUGUGGACAGCAAC___AA_________UAACAACAACGAACGCCUGCACCAGAUACUCAAAGGAUCCGGAGCAGGAUCGGGAG
.........((((((.(((.....))).....)))))).............................(((...(((((.((.(((.((....))))).)).))))).))).... (-18.36 = -19.25 +   0.89)

alignment

secondary structure

dotplot

Window 5

Location	5,472,336 – 5,472,438
Length	102
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	81.45
Mean single sequence MFE	-32.62
Consensus MFE	-21.95
Energy contribution	-22.04
Covariance contribution	0.09
Combinations/Pair	1.28
Mean z-score	-1.65
Structure conservation index	0.67
SVM decision value	0.26
SVM RNA-class probability	0.656075
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5472336 102 - 20766785
CUCCCGAUCCUGCUCCGGAUCCCUUGAGUAUCUGGUGCAGGCGUUCGUUGUUGUUG---------CU---AUUGCUGUCCACAUUAUGCAGAUAACGCUGUGGACUUUGAGUCU
(((.(((.(((((.((((((.(.....).)))))).)))))...)))........(---------(.---...)).(((((((....((.......)))))))))...)))... ( -31.10)
>DroSec_CAF1 1 100 - 1
UUCCCGAUCCUGCUCCGGAUCCCUUGAGUAUCUGGUGCAGGCGUUCGUUGUUGUUA---------UU---AUUGCUGUCCACAUUAUGCAGAUAACGCGAUGGACUUUGAGU--
........(((((.((((((.(.....).)))))).))))).(((((((((.((((---------((---..(((............)))))))))))))))))).......-- ( -32.20)
>DroSim_CAF1 3 102 - 1
CUCCCGAUCCUGCUCCGGAUCCCUUGAGUAUCUGGUGCAGGCGUUCGUUGUUGUUA---------UU---AUUGCUGUCCACAUUAUGCAGAUAACGCGAUGGACUUUGAGUCU
(((.....(((((.((((((.(.....).)))))).))))).(((((((((.((((---------((---..(((............))))))))))))))))))...)))... ( -33.50)
>DroEre_CAF1 2 102 - 1
CACCCGAUCCUGCUCCAGAUCCUUUGAGAAUUUGCUGCAGGCGUUCGUUGUUGUUA---------CU---GCUGUUGUCCACAUUAUGCAGAUAACGCUGCGAACUUUGAGUCU
.....((((((((..(((((.(.....).)))))..))))).((((((.((.((((---------((---((...((....))....)))).)))))).)))))).....))). ( -29.50)
>DroYak_CAF1 3 102 - 1
CACCCGAUCCUGCCCCGGAUCCUUUGAGAAUCUGGUGCAGGCGUUCGUUGUUGUUA---------CU---GUUGUUGUCCGCAUUCUGCAGAUAACGCGGCGGACUUUGAGUCU
.....((((((((.((((((.(.....).)))))).))))).(((((((((.((((---------((---((...((....))....)))).))))))))))))).....))). ( -35.70)
>DroPer_CAF1 306 108 - 1
------AGCCGGCUCCGGCUCCUUUGAGGAUCUGCUGCAGUCUCUCGUUGUUGUUGAUGCUGGCAUUGUUGCUGAUGUCAAUGUUUUGCAGAUAACGCGGCGAACUUUGACUCU
------.((((((..((((..(..(((((..(((...)))..)))))..)..))))..)))))).........((.(((((.(((((((.......)))..)))).))))))). ( -33.70)
>consensus
CUCCCGAUCCUGCUCCGGAUCCCUUGAGUAUCUGGUGCAGGCGUUCGUUGUUGUUA_________CU___AUUGCUGUCCACAUUAUGCAGAUAACGCGGCGGACUUUGAGUCU
........(((((.((((((.(.....).)))))).))))).(((((((((.((((...............((((............)))).)))))))))))))......... (-21.95 = -22.04 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:19 2006