Locus 6737

Sequence ID 3R_DroMel_CAF1
Location 17,754,177 – 17,754,308
Length 131
Max. P 0.943850
window10940 window10941 window10942

overview

Window 0

Location 17,754,177 – 17,754,278
Length 101
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 81.74
Mean single sequence MFE -23.45
Consensus MFE -14.04
Energy contribution -15.17
Covariance contribution 1.13
Combinations/Pair 1.09
Mean z-score -2.14
Structure conservation index 0.60
SVM decision value 0.28
SVM RNA-class probability 0.665116
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17754177 101 - 27905053
ACGCACUC---ACACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUAAAUUGCCAUUAGGGCAUACAACUCAAUCAGAAU
....((((---((((((.(((((.((((.........)))))))))...))..)))))))).............((((.....))))................. ( -24.10)
>DroSec_CAF1 43048 101 - 1
ACGCACUC---ACACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUAAAUUGCCAUUAGGGCAUACAGCUCAAUCAGAAU
..((((((---((((((.(((((.((((.........)))))))))...))..)))))))).............((((.....))))....))........... ( -26.30)
>DroSim_CAF1 42862 101 - 1
ACGCACUC---AAACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUAAAUUGCCAUUAGGGCAUACAGCUCAAUCAGAAU
..((.((.---.((((((..........))))))..))))((((((....((((((((((...)))).......((((.....))))))))))..))))))... ( -25.30)
>DroEre_CAF1 45447 89 - 1
---------------CAGAAUCACAGCCAUGUUGCUAGGCUUGAUUCACUGCUGUGUGAGUAACUCAAUUAAAUUGCCAUUAGGGCAUACAGCUCAAUCAGAAU
---------------..((((((.((((.........))))))))))...((((((((((...)))).......((((.....))))))))))........... ( -25.90)
>DroYak_CAF1 45955 104 - 1
ACCCAGUGAGUACAUCACAAUCACAGCCAUGUUGCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUAAAUUGCCAUUAGGGCAUACAGCUCAAUCAGCAU
.....((((.....))))(((((.((((.........)))))))))...(((((..(((((.............((((.....))))....)))))..))))). ( -26.63)
>DroPer_CAF1 46484 86 - 1
ACGCAUCU---GU------AU--CUGCCAG-----UAUGCAU-AUCUAAUGCUCUGAGACUAACUCAAUUAAAUUUCCAUUAGGGCCUACGACUCAAUCA-AAU
..((((((---(.------..--....)))-----.))))..-.......(((((((......................)))))))..............-... ( -12.45)
>consensus
ACGCACUC___ACACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUAAAUUGCCAUUAGGGCAUACAGCUCAAUCAGAAU
..................(((((.((((.........)))))))))....((((((((((...))).........(((.....))))))))))........... (-14.04 = -15.17 +   1.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,754,210 – 17,754,308
Length 98
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 71.82
Mean single sequence MFE -28.30
Consensus MFE -14.22
Energy contribution -15.40
Covariance contribution 1.18
Combinations/Pair 1.05
Mean z-score -1.53
Structure conservation index 0.50
SVM decision value -0.03
SVM RNA-class probability 0.519983
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17754210 98 + 27905053
UAAUUGAGUUACUCACACAGCAGUAAAUCAAGCCUAGAACCAUGGCUGUGAUUAUGGUGU---GAGUGCGUGUUUUUCA----------GUGUGUGUGGCAAAUCGGUUCA
.(((((((((((.(((((.(((.(((((((((((.........)))).))))).)).)))---(((.........))).----------))))).)))))...)))))).. ( -26.10)
>DroPse_CAF1 46562 90 + 1
UAAUUGAGUUAGUCUCAGAGCAUUAGAU-AUGCAUA-----CUGGCAG--AU------AC---AGAUGCGUGCC--GCAUUCGGUUC--GUGUGUGUCUCUGUGCUGAUGA
.......((((((..(((.((((.....-))))...-----)))((((--(.------((---(.(((((.(((--(....)))).)--)))).))).))))))))))).. ( -29.40)
>DroSec_CAF1 43081 108 + 1
UAAUUGAGUUACUCACACAGCAGUAAAUCAAGCCUAGAACCAUGGCUGUGAUUAUGGUGU---GAGUGCGUGUUUUUCAGUGUGUUUCAGUGUGUGUGGCAAAUCGGUUCA
.(((((((((((.(((((.(((.(((((((((((.........)))).))))).)).)))---(((.(((..(......)..)))))).))))).)))))...)))))).. ( -29.30)
>DroSim_CAF1 42895 108 + 1
UAAUUGAGUUACUCACACAGCAGUAAAUCAAGCCUAGAACCAUGGCUGUGAUUAUGGUUU---GAGUGCGUGUUUUUCAGUGGGUUUCAGUGUGUGUGGCAAAUCGGUUCA
.((((((.....(((((((.((.((((((..((((.(((((((((......)))))))))---.)).)).((.....))...))))).).)))))))))....)))))).. ( -26.40)
>DroEre_CAF1 45480 78 + 1
UAAUUGAGUUACUCACACAGCAGUGAAUCAAGCCUAGCAACAUGGCUGUGAUUCUG---------------------------------GUGUGUGUGGCAAAUCUGUUCA
.......(((((.(((((......((((((((((.........)))).))))))..---------------------------------))))).)))))........... ( -24.90)
>DroYak_CAF1 45988 109 + 1
UAAUUGAGUUACUCACACAGCAGUAAAUCAAGCCUAGCAACAUGGCUGUGAUUGUGAUGUACUCACUGGGUGUGUUUCAGUGUAUGU--GUGUGUGUGGCAAAUCGGUUCA
.(((((((((((.(((((((((...(((((((((.........)))).)))))....)))...(((((((.....)))))))....)--))))).)))))...)))))).. ( -33.70)
>consensus
UAAUUGAGUUACUCACACAGCAGUAAAUCAAGCCUAGAACCAUGGCUGUGAUUAUGGUGU___GAGUGCGUGUUUUUCAGUG_GUUU__GUGUGUGUGGCAAAUCGGUUCA
.......(((((.(((((.......(((((((((.........)))).))))).................((.....))..........))))).)))))........... (-14.22 = -15.40 +   1.18)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,754,210 – 17,754,308
Length 98
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 71.82
Mean single sequence MFE -21.86
Consensus MFE -11.42
Energy contribution -12.93
Covariance contribution 1.52
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.52
SVM decision value 1.34
SVM RNA-class probability 0.943850
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17754210 98 - 27905053
UGAACCGAUUUGCCACACACAC----------UGAAAAACACGCACUC---ACACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUA
......((.((((((((((((.----------((((...((.((.((.---..(((((..........)))))...)))).)).)))).)).)))))).)))).))..... ( -21.00)
>DroPse_CAF1 46562 90 - 1
UCAUCAGCACAGAGACACACAC--GAACCGAAUGC--GGCACGCAUCU---GU------AU--CUGCCAG-----UAUGCAU-AUCUAAUGCUCUGAGACUAACUCAAUUA
.....(((.(((((.((.....--...(((....)--))...((((((---(.------..--....)))-----.))))..-......))))))).).)).......... ( -16.70)
>DroSec_CAF1 43081 108 - 1
UGAACCGAUUUGCCACACACACUGAAACACACUGAAAAACACGCACUC---ACACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUA
......((.((((((((((((.((.....)).))........(((...---.......(((((.((((.........)))))))))...))))))))).)))).))..... ( -20.42)
>DroSim_CAF1 42895 108 - 1
UGAACCGAUUUGCCACACACACUGAAACCCACUGAAAAACACGCACUC---AAACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUA
......((.((((((((((((.((((......(....).((.((.((.---.((((((..........))))))..)))).)).)))).)).)))))).)))).))..... ( -22.00)
>DroEre_CAF1 45480 78 - 1
UGAACAGAUUUGCCACACACAC---------------------------------CAGAAUCACAGCCAUGUUGCUAGGCUUGAUUCACUGCUGUGUGAGUAACUCAAUUA
......((.((((((((((((.---------------------------------..((((((.((((.........))))))))))..)).)))))).)))).))..... ( -24.60)
>DroYak_CAF1 45988 109 - 1
UGAACCGAUUUGCCACACACAC--ACAUACACUGAAACACACCCAGUGAGUACAUCACAAUCACAGCCAUGUUGCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUA
......((.(((((((((((..--.....(((((.........)))))((((.((((.......((((.........)))))))).))))).)))))).)))).))..... ( -26.41)
>consensus
UGAACCGAUUUGCCACACACAC__AAAC_CACUGAAAAACACGCACUC___ACACCAUAAUCACAGCCAUGGUUCUAGGCUUGAUUUACUGCUGUGUGAGUAACUCAAUUA
......((.((((((((((((...........((.....)).................(((((.((((.........)))))))))...)).)))))).)))).))..... (-11.42 = -12.93 +   1.52)

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 12:28:43 2006