Locus 4464

Sequence ID 2R_DroMel_CAF1
Location 14,678,862 – 14,678,992
Length 130
Max. P 0.894829
window7138 window7139 window7140

overview

Window 8

Location 14,678,862 – 14,678,967
Length 105
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 77.59
Mean single sequence MFE -22.36
Consensus MFE -15.53
Energy contribution -16.60
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -1.56
Structure conservation index 0.69
SVM decision value 0.11
SVM RNA-class probability 0.590496
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14678862 105 + 20766785
GAUCAAUAAAAAAUAUAU------------U-UUUUAGAAACCAUGUUGCGCAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACGACAAAUAUCGAUAA
......(((((((....)------------)-)))))....(((((((..(((....((((.....))))....)))...))))))).((((((((.............)))))))). ( -22.72)
>DroSim_CAF1 5040 111 + 1
---UGAUAAGAAAUAUAUU---GACCGAAUU-UUUUACAAACCAUGUUGCGCAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACGACAAAUAUCGAUAA
---((.((((((((.....---......)))-)))))))..(((((((..(((....((((.....))))....)))...))))))).((((((((.............)))))))). ( -23.32)
>DroEre_CAF1 8491 111 + 1
G----AGAAAAAAUUUAGUCUUGAUCGAAUUUC---AGCAACCAUGUUGCGCAACAUUUGCAUGGAGCAACAAGUGCCUAAACAUUGUUCUCGAUACCAAUAGGACAAGUAUCGAUAA
(----((((....(((((.((((..........---.(((((...)))))((..(((....)))..))..))))...))))).....)))))(((((...........)))))..... ( -23.20)
>DroYak_CAF1 8718 114 + 1
G----AUAAUGAAAUUAAUUUUUUUCUAAUUUUUGUAGAAACCAUGUUGCGCAACAUUUUUAUGGAGCAACAAGUGCCUAAAAACGGCUAUCGAUACCAGACCGACAAAUAUCGAUAA
.----.................((((((.......))))))...((((((....(((....)))..))))))...(((.......)))((((((((.............)))))))). ( -20.22)
>consensus
G____AUAAAAAAUAUAUU___GAUCGAAUU_UUUUAGAAACCAUGUUGCGCAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACGACAAAUAUCGAUAA
.........................................(((((((..(((....((((.....))))....)))...))))))).((((((((.............)))))))). (-15.53 = -16.60 +   1.06)

alignment

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secondary structure

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Window 9

Location 14,678,862 – 14,678,967
Length 105
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 77.59
Mean single sequence MFE -25.50
Consensus MFE -20.44
Energy contribution -21.13
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -1.72
Structure conservation index 0.80
SVM decision value 0.98
SVM RNA-class probability 0.894829
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14678862 105 - 20766785
UUAUCGAUAUUUGUCGUCUUGGUAUCGAUAGCCAUGUUUAGGCACUUGUUGCUCCCUGCAAAUGUUGCGCAACAUGGUUUCUAAAA-A------------AUAUAUUUUUUAUUGAUC
.((((((((((.........))))))))))((((((((...(((....((((.....))))....)))..))))))))...(((((-(------------(....)))))))...... ( -26.30)
>DroSim_CAF1 5040 111 - 1
UUAUCGAUAUUUGUCGUCUUGGUAUCGAUAGCCAUGUUUAGGCACUUGUUGCUCCCUGCAAAUGUUGCGCAACAUGGUUUGUAAAA-AAUUCGGUC---AAUAUAUUUCUUAUCA---
.((((((((((.........))))))))))((((((((...(((....((((.....))))....)))..))))))))........-.........---................--- ( -25.60)
>DroEre_CAF1 8491 111 - 1
UUAUCGAUACUUGUCCUAUUGGUAUCGAGAACAAUGUUUAGGCACUUGUUGCUCCAUGCAAAUGUUGCGCAACAUGGUUGCU---GAAAUUCGAUCAAGACUAAAUUUUUUCU----C
...((((((((.........))))))))(((....(((((((((....((((.....))))....)))(((((...))))).---...............))))))...))).----. ( -25.80)
>DroYak_CAF1 8718 114 - 1
UUAUCGAUAUUUGUCGGUCUGGUAUCGAUAGCCGUUUUUAGGCACUUGUUGCUCCAUAAAAAUGUUGCGCAACAUGGUUUCUACAAAAAUUAGAAAAAAAUUAAUUUCAUUAU----C
.(((((((((..(.....)..)))))))))(((.......))).(.((((((.(.(((....))).).)))))).).((((((.......)))))).................----. ( -24.30)
>consensus
UUAUCGAUAUUUGUCGUCUUGGUAUCGAUAGCCAUGUUUAGGCACUUGUUGCUCCAUGCAAAUGUUGCGCAACAUGGUUUCUAAAA_AAUUCGAUC___AAUAAAUUUUUUAU____C
.((((((((((.........))))))))))((((((((...(((....((((.....))))....)))..))))))))........................................ (-20.44 = -21.13 +   0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,678,887 – 14,678,992
Length 105
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 84.25
Mean single sequence MFE -22.86
Consensus MFE -15.66
Energy contribution -16.70
Covariance contribution 1.04
Combinations/Pair 1.05
Mean z-score -2.02
Structure conservation index 0.69
SVM decision value 0.52
SVM RNA-class probability 0.766657
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14678887 105 + 20766785
AAACCAUGUUGCGCAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACGACAAAUAUCGAUAAUU----------UUUCUUCUACUCUUUUAACAUUA
...(((((((..(((....((((.....))))....)))...))))))).((((((((.............))))))))...----------....................... ( -21.62)
>DroSec_CAF1 9996 115 + 1
AAACCAUGUUGCACAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACUACAAAUAUCGAUAUAUUCCCAUGCUCUCUCUCCUACUCUUUUAACAUUA
.....((((((((.......)))((((((((......(((.......)))((((((((.............))))))))........)))))))).............))))).. ( -24.62)
>DroSim_CAF1 5071 115 + 1
AAACCAUGUUGCGCAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACGACAAAUAUCGAUAAUUUCCCACGUACUCUCUGCUACUCUGUUAACAUUA
.....((((((.(((......((((((((..((....(((.......)))((((((((.............)))))))).........)).)))))))).....))))))))).. ( -27.52)
>DroEre_CAF1 8522 114 + 1
CAACCAUGUUGCGCAACAUUUGCAUGGAGCAACAAGUGCCUAAACAUUGUUCUCGAUACCAAUAGGACAAGUAUCGAUAACCGCCCAUGUUCUCUC-UUUACUCUUUUAACAUUC
.....(((((....)))))..((((((.(((((((((......)).))))).(((((((...........))))))).....))))))))......-.................. ( -21.90)
>DroYak_CAF1 8752 114 + 1
AAACCAUGUUGCGCAACAUUUUUAUGGAGCAACAAGUGCCUAAAAACGGCUAUCGAUACCAGACCGACAAAUAUCGAUAACACCCCA-GUUCUCUCCUUUACGCUUUUAACAUUC
.....((((((.((..(((....)))(((.(((....(((.......)))((((((((.............))))))))........-))))))........))...)))))).. ( -18.62)
>consensus
AAACCAUGUUGCGCAACAUUUGCAGGGAGCAACAAGUGCCUAAACAUGGCUAUCGAUACCAAGACGACAAAUAUCGAUAACUUCCCA_GUUCUCUCUUCUACUCUUUUAACAUUA
...(((((((..(((....((((.....))))....)))...))))))).((((((((.............)))))))).................................... (-15.66 = -16.70 +   1.04)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:23 2006