Locus 4616

Sequence ID 2L_DroMel_CAF1
Location 13,195,605 – 13,195,710
Length 105
Max. P 0.956165
window7289 window7290

overview

Window 9

Location 13,195,605 – 13,195,710
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 78.13
Mean single sequence MFE -26.61
Consensus MFE -17.92
Energy contribution -17.42
Covariance contribution -0.50
Combinations/Pair 1.25
Mean z-score -1.67
Structure conservation index 0.67
SVM decision value 0.86
SVM RNA-class probability 0.868309
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13195605 105 + 22407834
UGGGACUGCAAUUUAUGCAGGAGAUGCUUGAGCUGACCAAGAUGCAAAGCAUAAAUCAGCUAGCGCAACUGCAGGUUUGCAUGCUUUAUACAUUUUAAAUGGAAA
.(((..(((((....(((((..(.((((..((((((.....((((...))))...)))))))))))..)))))...)))))..)))................... ( -28.40)
>DroVir_CAF1 2162 92 + 1
UGGGACUGCAGUUUAUGCAGGAAAUGCUUGAGCUCACCAAAAUGCAAAGCAUGAAUCAGCUGGCACAGCUGCAGGUGCGUAAAU-----------AAAAAAAU--
..........(((((((((....((((((..((..........)).))))))....((((((...))))))....)))))))))-----------........-- ( -23.00)
>DroGri_CAF1 2267 91 + 1
UGGGCUUGCAGUUUAUGCAGGAAAUGUUGGAGCUGACCAAAAUGCAGAGCAUGAAUCAACUGGCCCAGCUGCAGGUGCGUAAAU-----------UACAAGA---
....((((.((((((((((......(((((.(((.......((((...)))).........))))))))......)))))))))-----------).)))).--- ( -26.09)
>DroEre_CAF1 5875 100 + 1
UGGGACUGCAAUUUAUGCAGGAGAUGCUUGAGCUGACCAAGAUGCAGAGCAUAAAUCAGCUAGCGCAACUGCAGGUUUGUAUGCUUU----AUUUUAAAGGG-AA
.(((..(((((....(((((..(.((((..((((((.....((((...))))...)))))))))))..)))))...)))))..))).----...........-.. ( -26.40)
>DroYak_CAF1 2937 100 + 1
UGGGACUGCAAUUUAUGCAGGAGAUGCUUGAGCUGACCAAGAUGCAAAGCAUAAAUCAGCUAGCGCAACUGCAGGUUUGUAUGCUUC----AUUUUAAAUGG-AA
(((..((((((....(((((..(.((((..((((((.....((((...))))...)))))))))))..)))))...))))).)..))----)..........-.. ( -27.00)
>DroMoj_CAF1 2166 94 + 1
UGGGCUUGCAGUUCAUGCAGGAAAUGCUGGAGCUAACCAAAAUGCAGAGCAUGAACCAGCUGGCACAGCUGCAGGUGCGUAACU-----------CAAAUGAUAA
.(.((((((.((((((((......((((((......)))....)))..)))))))).(((((...))))))))))).)......-----------.......... ( -28.80)
>consensus
UGGGACUGCAAUUUAUGCAGGAAAUGCUUGAGCUGACCAAAAUGCAAAGCAUAAAUCAGCUAGCGCAACUGCAGGUGCGUAAGC___________UAAAUGA_AA
......(((.(..(.(((((....((((..((((((.....((((...))))...))))))))))...))))).)..))))........................ (-17.92 = -17.42 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,195,605 – 13,195,710
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 78.13
Mean single sequence MFE -23.80
Consensus MFE -18.17
Energy contribution -17.95
Covariance contribution -0.22
Combinations/Pair 1.20
Mean z-score -2.01
Structure conservation index 0.76
SVM decision value 1.46
SVM RNA-class probability 0.956165
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13195605 105 - 22407834
UUUCCAUUUAAAAUGUAUAAAGCAUGCAAACCUGCAGUUGCGCUAGCUGAUUUAUGCUUUGCAUCUUGGUCAGCUCAAGCAUCUCCUGCAUAAAUUGCAGUCCCA
.....................(((((((....))))..)))(((((((((((.((((...))))...))))))))..))).....(((((.....)))))..... ( -27.40)
>DroVir_CAF1 2162 92 - 1
--AUUUUUUU-----------AUUUACGCACCUGCAGCUGUGCCAGCUGAUUCAUGCUUUGCAUUUUGGUGAGCUCAAGCAUUUCCUGCAUAAACUGCAGUCCCA
--........-----------.......((((..((((((...))))))....((((...))))...)))).((....)).....(((((.....)))))..... ( -20.40)
>DroGri_CAF1 2267 91 - 1
---UCUUGUA-----------AUUUACGCACCUGCAGCUGGGCCAGUUGAUUCAUGCUCUGCAUUUUGGUCAGCUCCAACAUUUCCUGCAUAAACUGCAAGCCCA
---.......-----------......((....))....((((.((((((((.((((...))))...))))))))...........((((.....)))).)))). ( -20.70)
>DroEre_CAF1 5875 100 - 1
UU-CCCUUUAAAAU----AAAGCAUACAAACCUGCAGUUGCGCUAGCUGAUUUAUGCUCUGCAUCUUGGUCAGCUCAAGCAUCUCCUGCAUAAAUUGCAGUCCCA
..-...........----...(((........)))((.(((...((((((((.((((...))))...))))))))...))).)).(((((.....)))))..... ( -24.60)
>DroYak_CAF1 2937 100 - 1
UU-CCAUUUAAAAU----GAAGCAUACAAACCUGCAGUUGCGCUAGCUGAUUUAUGCUUUGCAUCUUGGUCAGCUCAAGCAUCUCCUGCAUAAAUUGCAGUCCCA
..-...........----...(((........)))((.(((...((((((((.((((...))))...))))))))...))).)).(((((.....)))))..... ( -24.60)
>DroMoj_CAF1 2166 94 - 1
UUAUCAUUUG-----------AGUUACGCACCUGCAGCUGUGCCAGCUGGUUCAUGCUCUGCAUUUUGGUUAGCUCCAGCAUUUCCUGCAUGAACUGCAAGCCCA
..........-----------......(((....((((((...))))))((((((((........((((......))))........)))))))))))....... ( -25.09)
>consensus
UU_CCAUUUA___________ACAUACAAACCUGCAGCUGCGCCAGCUGAUUCAUGCUCUGCAUCUUGGUCAGCUCAAGCAUCUCCUGCAUAAACUGCAGUCCCA
................................(((((.(((...((((((((.((((...))))...))))))))...)))....)))))............... (-18.17 = -17.95 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:41 2006