Locus 5944

Sequence ID 3L_DroMel_CAF1
Location 15,922,224 – 15,922,418
Length 194
Max. P 0.781498
window9494 window9495

overview

Window 4

Location 15,922,224 – 15,922,344
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -35.66
Consensus MFE -28.21
Energy contribution -28.41
Covariance contribution 0.20
Combinations/Pair 1.31
Mean z-score -1.19
Structure conservation index 0.79
SVM decision value 0.02
SVM RNA-class probability 0.543672
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15922224 120 + 23771897
AGUGGCUAACCCGCCAGCCCACUUGUCCGGUGGAUCGAAAUUCCCUGACUACUGCCAACUUGCGGGCAGUGCCUCGCAUAUUGCGCAACCUACUGUCCAGGUGAGAAAAACCCAACGCCU
..((((......))))...((((((..((((((.(((........)))....((((((..(((((((...))).))))..))).)))..))))))..))))))................. ( -36.80)
>DroVir_CAF1 3605 106 + 1
AAUGGCUAACACGCCAGCCCACAUGUCCCGUAGAUCGCAAUGCACUAACUACCGCGAAUUUGCGAGCAGUGCCGCGCAUAUUGCGCAACUUGUUGUCCAGGUAGGU--------------
..((((......))))((((((.(((..((((((((((...............))).))))))).))))))..((((.....)))).(((((.....))))).)))-------------- ( -30.56)
>DroSim_CAF1 24267 120 + 1
AGUGGCUAACCCGCCAGCCCACUUGUCCGGUGGAUCGCAAUGCCUUGACCACUGCCAACUUGCGAGCAGUGCCUCGCAUAUUGCGCAACCUACUGUCCAGGUGAGAAACACCCAACGCCU
..((((......))))...((((((..((((((..(((((((...(((.(((((((.......).))))))..)))..)))))))....))))))..))))))................. ( -37.30)
>DroEre_CAF1 21606 120 + 1
AGUGGCUAACCCGCCAGCCCACUUGUCCGGUGGAUCGCAAUGCCCUGACAACUGCCAACUUGCGGGCAGUUCCUCGCAUAUUGCGCAACCUACUGUCCAGGUGAGAACCACCCAACGCCU
..((((......))))...((((((..((((((..(((((((...(((.(((((((........)))))))..)))..)))))))....))))))..))))))................. ( -39.40)
>DroYak_CAF1 22212 120 + 1
AGUGGCUAACCCGCCAGCCCACCUGUCCGGUGGAUCGCAAUGCCCUGACUACUGCCAACUUGCGGGCAGUGCCUCGCAUAUUGCGCAACCUACUGUCCAGGUGAGAACCAACCAACCUAC
..((((......))))...((((((..((((((..(((((((...(((.(((((((........)))))))..)))..)))))))....))))))..))))))................. ( -42.20)
>DroMoj_CAF1 2004 106 + 1
AAUGGCUGACACGCCAGCCCACAUGCCCAGUUGAUCGUAAUGCCCUAACUACUGCAAAUCUGCGAGCUGUGCCGCGCAUAUUGCGCAACUUGUUGUCCAGGUAACU--------------
...(((((......))))).....((.((((...(((((.(((..........)))....))))))))).)).((((.....)))).(((((.....)))))....-------------- ( -27.70)
>consensus
AGUGGCUAACCCGCCAGCCCACUUGUCCGGUGGAUCGCAAUGCCCUGACUACUGCCAACUUGCGAGCAGUGCCUCGCAUAUUGCGCAACCUACUGUCCAGGUGAGAA_CACCCAACGCCU
..((((......))))...((((((..((((((..(((((((.......((((((..........)))))).......)))))))....))))))..))))))................. (-28.21 = -28.41 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,922,304 – 15,922,418
Length 114
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.90
Mean single sequence MFE -20.03
Consensus MFE -16.03
Energy contribution -15.45
Covariance contribution -0.58
Combinations/Pair 1.24
Mean z-score -1.28
Structure conservation index 0.80
SVM decision value 0.56
SVM RNA-class probability 0.781498
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15922304 114 + 23771897
UUGCGCAACCUACUGUCCAGGUGAGAAAAACCCAACGCCUUCUACUCUGUGAACCUUGUG----GACUCUAACUAAUCUUUGACCCUUGCCAACCAGACUGUCAAUCACCUGUGACAA
.............(((((((((((................(((((...(....)...)))----)).............(((((..(((.....)))...)))))))))))).)))). ( -23.90)
>DroSec_CAF1 24016 113 + 1
UUGCGCAACCUACUGUCCAGGUGAGAAACACCCAACGCCUCCUACUCUAC-GCCCUUGUA----AACCCUAACUAAUCUUUGACCCUUGCCAACCAGACUGUCAAUUACCUGUGACAA
.............(((((((((((.......................(((-(....))))----...............(((((..(((.....)))...)))))))))))).)))). ( -17.20)
>DroSim_CAF1 24347 113 + 1
UUGCGCAACCUACUGUCCAGGUGAGAAACACCCAACGCCUCCUACUCUCC-ACCCUUGUG----AACCGUAACUAAUCUUUGACCCUUGCCAACCAGACUGUCAAUUACCUGUGACAA
.............(((((((((((..................(((....(-((....)))----....)))........(((((..(((.....)))...)))))))))))).)))). ( -18.40)
>DroEre_CAF1 21686 113 + 1
UUGCGCAACCUACUGUCCAGGUGAGAACCACCCAACGCCUUUAACUCUCC-ACCCUUGUG----AAACCUAACUAAUCUUUGACCCCUGCCAACCAGACUGUCAAUUACCUGUGACAA
.............(((((((((((.........................(-((....)))----...............(((((..(((.....)))...)))))))))))).)))). ( -20.40)
>DroYak_CAF1 22292 113 + 1
UUGCGCAACCUACUGUCCAGGUGAGAACCAACCAACCUACUUAACUCUCC-ACCCUUGUG----AGCCCUAACUAAUCUUUGACCCCUGCCCACCAGACUGUCAAUUACCUGUGACAA
.............(((((((((((......................((((-(....)).)----)).............(((((..(((.....)))...)))))))))))).)))). ( -20.70)
>DroMoj_CAF1 2084 97 + 1
UUGCGCAACUUGUUGUCCAGGUAACU--------------CUUUUGCACG-ACUCUUGUUUUUCAUACCUAGCUAA----UGAGCGUUUUCA--CAGGCUCUCAAUUACCUGCGACAA
............((((((((((((..--------------.........(-((....)))................----((((.(((....--..))).)))).))))))).))))) ( -19.60)
>consensus
UUGCGCAACCUACUGUCCAGGUGAGAAACACCCAACGCCUCCUACUCUCC_ACCCUUGUG____AACCCUAACUAAUCUUUGACCCUUGCCAACCAGACUGUCAAUUACCUGUGACAA
.............(((((((((((.................................((............))......(((((..(((.....)))...)))))))))))).)))). (-16.03 = -15.45 +  -0.58)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:48 2006