Locus 1662

Sequence ID 2R_DroMel_CAF1
Location 6,282,519 – 6,282,694
Length 175
Max. P 0.966536
window2775 window2776 window2777 window2778 window2779

overview

Window 5

Location 6,282,519 – 6,282,618
Length 99
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 64.13
Mean single sequence MFE -22.02
Consensus MFE -11.22
Energy contribution -12.17
Covariance contribution 0.95
Combinations/Pair 1.16
Mean z-score -1.55
Structure conservation index 0.51
SVM decision value 0.34
SVM RNA-class probability 0.695173
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6282519 99 - 20766785
GUCACCCACACUAUCCAUGAACUUAUUUAUCUAUGGUAUAGAUAUAUGGGCAUCUGGAGGUGACAGACAUAUU-UUUAAGGCUACUU---------------AAUUCCACACUCG
((((((.......((((.((.(((((.(((((((...))))))).)))))..)))))))))))).........-.(((((....)))---------------))........... ( -23.01)
>DroSec_CAF1 25111 95 - 1
GUCACCCACACUAUCCAUAAACUUAUUUAUCUAUGAGAUAGAUAUUUUGGUAUCUGCAGCUGACUGACGGAUU-UUUAAGGCUAU-------------------CGCCACAUUUA
..............(((......((((((((.....))))))))...))).((((((((....))).))))).-.....(((...-------------------.)))....... ( -17.90)
>DroEre_CAF1 24891 106 - 1
GUCACCCACACUUUCCUGCAACCUAUAGA---------UAUGUAUAUGGGCACCAGGAGGUGACUGAUGGAUUUUUUGAGGCAACCUCCAACAUUUACUUACAAUUCCACACUCG
((((((.......(((((...((((((..---------......))))))...)))))))))))((.((((..((.((((.................)))).)).)))))).... ( -25.14)
>consensus
GUCACCCACACUAUCCAUAAACUUAUUUAUCUAUG__AUAGAUAUAUGGGCAUCUGGAGGUGACUGACGGAUU_UUUAAGGCUAC_U_______________AAUUCCACACUCG
((((((..((....(((......((((((((.....))))))))...)))....))..))))))................................................... (-11.22 = -12.17 +   0.95)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,282,544 – 6,282,658
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 75.90
Mean single sequence MFE -30.05
Consensus MFE -17.19
Energy contribution -18.13
Covariance contribution 0.94
Combinations/Pair 1.20
Mean z-score -2.32
Structure conservation index 0.57
SVM decision value 1.60
SVM RNA-class probability 0.966536
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6282544 114 + 20766785
A-AAUAUGUCUGUCACCU-----CCAGAUGCCCAUAUAUCUAUACCAUAGAUAAAUAAGUUCAUGGAUAGUGUGGGUGACAAGUCAGCGUAGCAAACUCUGAUUGAUGUUGAUGCAAUUG
.-....(((.(((((((.-----.((((((......)))))...((((..((......))..)))).....)..))))))).((((((((..((.....))....))))))))))).... ( -28.00)
>DroSec_CAF1 25132 114 + 1
A-AAUCCGUCAGUCAGCU-----GCAGAUACCAAAAUAUCUAUCUCAUAGAUAAAUAAGUUUAUGGAUAGUGUGGGUGACAAGUCAGAGCAGCAAACUCUGAUUGAUGUUGAUGCAAUUG
.-.(((((((((((((((-----((....(((...(((.(((((.(((((((......))))))))))))))).)))((....))...)))))......)))))))))..)))....... ( -33.20)
>DroEre_CAF1 24931 106 + 1
AAAAUCCAUCAGUCACCU-----CCUGGUGCCCAUAUACAUA---------UCUAUAGGUUGCAGGAAAGUGUGGGUGACAAGUCACAGCAACCAGCUCUGAUUGAUGUUGAUGCAAUUG
......((((((((((((-----((((..(((.(((......---------..))).)))..))))).......)))))).(((((.(((.....))).))))).....)))))...... ( -29.81)
>DroYak_CAF1 28383 105 + 1
A-AAUCCAUCAGUCACCUACAGUCCAGGUCC-----UACACA---------UCUAUAAGUACAUGGAAAGUGUGGGUGACAAGUCAAAGCAACAAACUCUGAUUGAUGUUGAUGCAAUUG
.-....(((((((((((((((.((((.((.(-----(.....---------......)).)).))))...)))))))))).(((((.((.......)).))))).....)))))...... ( -29.20)
>consensus
A_AAUCCAUCAGUCACCU_____CCAGAUGCCCAUAUACAUA_________UAAAUAAGUUCAUGGAAAGUGUGGGUGACAAGUCAGAGCAACAAACUCUGAUUGAUGUUGAUGCAAUUG
......((((.(((((((.....(((...((...........................))...))).......))))))).(((((((((.....)))))))))))))............ (-17.19 = -18.13 +   0.94)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,282,544 – 6,282,658
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.90
Mean single sequence MFE -29.11
Consensus MFE -15.72
Energy contribution -16.96
Covariance contribution 1.25
Combinations/Pair 1.23
Mean z-score -2.35
Structure conservation index 0.54
SVM decision value 1.33
SVM RNA-class probability 0.942343
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6282544 114 - 20766785
CAAUUGCAUCAACAUCAAUCAGAGUUUGCUACGCUGACUUGUCACCCACACUAUCCAUGAACUUAUUUAUCUAUGGUAUAGAUAUAUGGGCAUCUGG-----AGGUGACAGACAUAUU-U
..................((((.((.....)).)))).((((((((.......((((.((.(((((.(((((((...))))))).)))))..)))))-----))))))))).......-. ( -26.51)
>DroSec_CAF1 25132 114 - 1
CAAUUGCAUCAACAUCAAUCAGAGUUUGCUGCUCUGACUUGUCACCCACACUAUCCAUAAACUUAUUUAUCUAUGAGAUAGAUAUUUUGGUAUCUGC-----AGCUGACUGACGGAUU-U
.......(((((...((((((((((.....))))))).))).........(((((((((............)))).))))).....)))))((((((-----((....))).))))).-. ( -24.20)
>DroEre_CAF1 24931 106 - 1
CAAUUGCAUCAACAUCAAUCAGAGCUGGUUGCUGUGACUUGUCACCCACACUUUCCUGCAACCUAUAGA---------UAUGUAUAUGGGCACCAGG-----AGGUGACUGAUGGAUUUU
............(((((.(((.(((.....))).)))...((((((.......(((((...((((((..---------......))))))...))))-----))))))))))))...... ( -32.91)
>DroYak_CAF1 28383 105 - 1
CAAUUGCAUCAACAUCAAUCAGAGUUUGUUGCUUUGACUUGUCACCCACACUUUCCAUGUACUUAUAGA---------UGUGUA-----GGACCUGGACUGUAGGUGACUGAUGGAUU-U
............(((((.(((((((.....)))))))...((((((.(((...((((.((.((((((..---------..))))-----)))).)))).))).)))))))))))....-. ( -32.80)
>consensus
CAAUUGCAUCAACAUCAAUCAGAGUUUGCUGCUCUGACUUGUCACCCACACUAUCCAUGAACUUAUAGA_________UAGAUAUAUGGGCACCUGG_____AGGUGACUGACGGAUU_U
............((((..(((((((.....)))))))...((((((........(((....((((((((((.....))))))))....))....)))......)))))).))))...... (-15.72 = -16.96 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,282,578 – 6,282,694
Length 116
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 81.10
Mean single sequence MFE -30.75
Consensus MFE -21.31
Energy contribution -23.25
Covariance contribution 1.94
Combinations/Pair 1.12
Mean z-score -2.18
Structure conservation index 0.69
SVM decision value 1.26
SVM RNA-class probability 0.937463
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6282578 116 + 20766785
UAUACCAUAGAUAAAUAAGUUCAUGGAUAGUGUGGGUGACAAGUCAGCGUAGCAAACUCUGAUUGAUGUUGAUGCAAUUGCAAUGCAAUUGCAAAUGGAAACACUUGAGCUGAUCG--
....((((..((......))..)))).((((.((((((....((((((((..((.....))....))))))))((((((((...)))))))).........)))))).))))....-- ( -30.40)
>DroSec_CAF1 25166 109 + 1
UAUCUCAUAGAUAAAUAAGUUUAUGGAUAGUGUGGGUGACAAGUCAGAGCAGCAAACUCUGAUUGAUGUUGAUGCAAUUGCAAUGCAGUUGCAAAUGGAAACACUUGAG---------
((((.(((((((......)))))))))))((((....((((((((((((.......))))))))..))))..(((((((((...))))))))).......)))).....--------- ( -32.70)
>DroEre_CAF1 24966 109 + 1
UA---------UCUAUAGGUUGCAGGAAAGUGUGGGUGACAAGUCACAGCAACCAGCUCUGAUUGAUGUUGAUGCAAUUGCAAUCCAGUUGCAAGUGGAAACACUUGAGCUGAUCGCC
..---------......((((((((....(((..(....)....))).(((..((((((.....)).)))).)))..))))))))(((((.((((((....)))))))))))...... ( -37.00)
>DroYak_CAF1 28417 107 + 1
CA---------UCUAUAAGUACAUGGAAAGUGUGGGUGACAAGUCAAAGCAACAAACUCUGAUUGAUGUUGAUGCAAUUGCAGUCCAGUUGCAAAUGGAAACACUUGAGCUGAUCG--
((---------((((((..(.......)..))))))))....(((((..(((((.....)).)))...)))))((....)).(..(((((.(((.((....)).))))))))..).-- ( -22.90)
>consensus
UA_________UAAAUAAGUUCAUGGAAAGUGUGGGUGACAAGUCAGAGCAACAAACUCUGAUUGAUGUUGAUGCAAUUGCAAUCCAGUUGCAAAUGGAAACACUUGAGCUGAUCG__
.................((((((.....(((((....(((((((((((((.....)))))))))..))))..((((((((.....)))))))).......)))))))))))....... (-21.31 = -23.25 +   1.94)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,282,578 – 6,282,694
Length 116
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 81.10
Mean single sequence MFE -23.88
Consensus MFE -16.95
Energy contribution -16.95
Covariance contribution -0.00
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.71
SVM decision value 0.62
SVM RNA-class probability 0.802435
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6282578 116 - 20766785
--CGAUCAGCUCAAGUGUUUCCAUUUGCAAUUGCAUUGCAAUUGCAUCAACAUCAAUCAGAGUUUGCUACGCUGACUUGUCACCCACACUAUCCAUGAACUUAUUUAUCUAUGGUAUA
--.(((.((.(((.((((...((..(((((((((...)))))))))..(((.((.....)))))))..))))))))).)))......(((((..(((((....)))))..)))))... ( -22.40)
>DroSec_CAF1 25166 109 - 1
---------CUCAAGUGUUUCCAUUUGCAACUGCAUUGCAAUUGCAUCAACAUCAAUCAGAGUUUGCUGCUCUGACUUGUCACCCACACUAUCCAUAAACUUAUUUAUCUAUGAGAUA
---------....(((((.......(((((.(((...))).))))).......((((((((((.....))))))).)))......))))).........(((((......)))))... ( -23.60)
>DroEre_CAF1 24966 109 - 1
GGCGAUCAGCUCAAGUGUUUCCACUUGCAACUGGAUUGCAAUUGCAUCAACAUCAAUCAGAGCUGGUUGCUGUGACUUGUCACCCACACUUUCCUGCAACCUAUAGA---------UA
(((((((((((((((((....)))))((((.((.....)).))))..............))))))))))))((((....))))........................---------.. ( -31.60)
>DroYak_CAF1 28417 107 - 1
--CGAUCAGCUCAAGUGUUUCCAUUUGCAACUGGACUGCAAUUGCAUCAACAUCAAUCAGAGUUUGUUGCUUUGACUUGUCACCCACACUUUCCAUGUACUUAUAGA---------UG
--..(((....((((((....))))))..((((((.(((....))).......((((((((((.....))))))).)))............)))).)).......))---------). ( -17.90)
>consensus
__CGAUCAGCUCAAGUGUUUCCAUUUGCAACUGCAUUGCAAUUGCAUCAACAUCAAUCAGAGUUUGCUGCUCUGACUUGUCACCCACACUAUCCAUGAACUUAUAGA_________UA
.............(((((.......(((((.((.....)).))))).......((((((((((.....))))))).)))......)))))............................ (-16.95 = -16.95 +  -0.00)

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 10:10:06 2006