Locus 10173

Sequence ID 3R_DroMel_CAF1
Location 27,303,000 – 27,303,195
Length 195
Max. P 0.951682
window16196 window16197 window16198

overview

Window 6

Location 27,303,000 – 27,303,118
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.19
Mean single sequence MFE -37.95
Consensus MFE -29.76
Energy contribution -30.02
Covariance contribution 0.25
Combinations/Pair 1.26
Mean z-score -2.35
Structure conservation index 0.78
SVM decision value 0.24
SVM RNA-class probability 0.650412
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27303000 118 - 27905053
AAUUGAGUGAUAACAGCUUUCGCUGUUGGCGGUUGUUAACAUCUAUAAAAUGGAAAGUGUCACAC-CAACGUGACGCCC-AAACAGCCUUGAAAGUGGUUGUUGUUUUUGAGCUGUCGGG
...........((((((....))))))(((((((...(((..........(((...(((((((..-....)))))))))-)(((((((........))))))))))....)))))))... ( -36.20)
>DroSec_CAF1 7975 118 - 1
AAUGGAGUGAUAACAGCUUUCGCUGUUGACAGCUGUUAGCGUCUAUAAAAUGGAAAGUGUCACAC-CAACGUGACGCCC-AAACAGCCUUGAAAGUGGUUGUUGUCUUCCAGCUGUCGGG
...........((((((....))))))((((((((..(((..........(((...(((((((..-....)))))))))-)(((((((........)))))))).))..))))))))... ( -44.00)
>DroSim_CAF1 8392 118 - 1
AAUGGAGUGAUAACAGCUUUCGCUGUUGACAGCUGUUAGCGUCUAUAAAAUGGAAAGUGUCACAC-CAACGUGACGCCC-AAACAGCCUUGAAAGUGGUUGUUGUCUUCCAGCUGUCGGG
...........((((((....))))))((((((((..(((..........(((...(((((((..-....)))))))))-)(((((((........)))))))).))..))))))))... ( -44.00)
>DroEre_CAF1 8244 118 - 1
AAUGGAGUGAUAACAGCUUUCGCUGUUGACGGCUGUUAAUGUCCAUAAAAUGGAAAGUGUCACAC-CAACGUGACGCCC-AAACAACCUUGAAAGUGGUUGUUGUCUUCGAGCUGGCGGG
.(((((....((((((((.(((....))).))))))))...)))))..........(((((((..-....)))))))((-.(((((((........)))))))(((........))))). ( -38.90)
>DroYak_CAF1 4293 118 - 1
AAUGGAGUGAUAACAGCUUUCGCUGUUGUCGGCUGUAAACGUUCAUAAAAUGGAAAGUGUCACAC-CAACGUGACGCCC-AAACAACCUUGAAAGUGGUUGUUGUCUUCCAGCUUUUGGG
..((.((((((((((((....))))))))).))).)).....(((.((..(((((.(((((((..-....)))))))..-.(((((((........)))))))...)))))..)).))). ( -40.50)
>DroAna_CAF1 9311 113 - 1
AAUUGAGCGAUAACUGCUUUCGCUAUUAACACCC------AUCUA-AAAAUGGAAAGUGUCACACACGACAUGACGCCCGAAACAGCCUUGAAACUGGUUUGUGUCAUCAAGUUGUUGGC
....(((((.....)))))..((((.((((..((------((...-...))))...(((((......)))))(((((..(((.(((........))).)))))))).....)))).)))) ( -24.10)
>consensus
AAUGGAGUGAUAACAGCUUUCGCUGUUGACAGCUGUUAACGUCUAUAAAAUGGAAAGUGUCACAC_CAACGUGACGCCC_AAACAGCCUUGAAAGUGGUUGUUGUCUUCCAGCUGUCGGG
...........((((((....))))))(((((((.......((((.....))))..(((((((.......)))))))....(((((((........))))))).......)))))))... (-29.76 = -30.02 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 27,303,040 – 27,303,155
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.23
Mean single sequence MFE -34.78
Consensus MFE -24.91
Energy contribution -25.38
Covariance contribution 0.48
Combinations/Pair 1.24
Mean z-score -2.30
Structure conservation index 0.72
SVM decision value 0.22
SVM RNA-class probability 0.640532
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27303040 115 + 27905053
-GGGCGUCACGUUG-GUGUGACACUUUCCAUUUUAUAGAUGUUAACAACCGCCAACAGCGAAAGCUGUUAUCACUCAAUUCCCAUA---UACCUUGUUCUUUGUUGUGGGACACCCACCU
-.(((((((((...-.))))))..((..((((.....))))..)).....)))((((((....))))))..........(((((((---...............)))))))......... ( -32.06)
>DroSec_CAF1 8015 115 + 1
-GGGCGUCACGUUG-GUGUGACACUUUCCAUUUUAUAGACGCUAACAGCUGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCUUA---UACCUGGUUUUUUGUUGUGGGACACCCACCU
-(((.(((....((-(.((((................(((((.....)).)))((((((....)))))).)))).)))...((...---.....)).............))).))).... ( -34.80)
>DroSim_CAF1 8432 115 + 1
-GGGCGUCACGUUG-GUGUGACACUUUCCAUUUUAUAGACGCUAACAGCUGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCUUA---UACCUGGUUCUUUGUUGUGGGACACCCACCU
-(((.(((....((-(.((((................(((((.....)).)))((((((....)))))).)))).)))...((...---.....)).............))).))).... ( -34.80)
>DroEre_CAF1 8284 115 + 1
-GGGCGUCACGUUG-GUGUGACACUUUCCAUUUUAUGGACAUUAACAGCCGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCAAA---UGUCUGGUUCUUUGUUGUGGGACACCCACUG
-.(((((((((...-.))))))....(((((...)))))........)))(((((((((....)))))).((((..((...(((..---....))).....))..)))))))........ ( -35.80)
>DroYak_CAF1 4333 115 + 1
-GGGCGUCACGUUG-GUGUGACACUUUCCAUUUUAUGAACGUUUACAGCCGACAACAGCGAAAGCUGUUAUCACUCCAUUCCCAAA---UAUCGUGUUCUUUGUUUUGGGACACCCACCU
-(((.(((..((((-((((((.((.(((........))).))))))).)))))((((((....))))))............(((((---...((.......)).)))))))).))).... ( -36.10)
>DroAna_CAF1 9351 112 + 1
CGGGCGUCAUGUCGUGUGUGACACUUUCCAUUUU-UAGAU------GGGUGUUAAUAGCGAAAGCAGUUAUCGCUCAAUUCUGAACCAUCAUCGGGGGCUUUGUUG-GGAACACCCACCG
((((((((((.......))))).....((...((-(((((------(((((.((((.((....)).)))).))))))..))))))((......)))))).....((-((....))))))) ( -35.10)
>consensus
_GGGCGUCACGUUG_GUGUGACACUUUCCAUUUUAUAGACGUUAACAGCCGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCAAA___UACCUGGUUCUUUGUUGUGGGACACCCACCU
.(((.((((((.....))))))...((((((......((((........))))((((((....))))))....................................))))))..))).... (-24.91 = -25.38 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 27,303,078 – 27,303,195
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.33
Mean single sequence MFE -30.97
Consensus MFE -14.34
Energy contribution -15.57
Covariance contribution 1.22
Combinations/Pair 1.12
Mean z-score -2.48
Structure conservation index 0.46
SVM decision value 1.41
SVM RNA-class probability 0.951682
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27303078 117 + 27905053
GUUAACAACCGCCAACAGCGAAAGCUGUUAUCACUCAAUUCCCAUA---UACCUUGUUCUUUGUUGUGGGACACCCACCUGUGGAUGAUCACCAGCUACUAGAUGAUUAUCCUUUCACUU
....(((......((((((....))))))..........(((((((---...............)))))))........)))(((((((((.(........).)))))))))........ ( -29.96)
>DroSec_CAF1 8053 117 + 1
GCUAACAGCUGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCUUA---UACCUGGUUUUUUGUUGUGGGACACCCACCUGCGGAUGAUCACCAGCUACUGGAUGAUGAUCCUUUCACUU
((.......((((((((((....)))))).((((..((...((...---.....)).....))..)))))))).......))((((.((((((((...)))).)))).))))........ ( -36.14)
>DroSim_CAF1 8470 117 + 1
GCUAACAGCUGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCUUA---UACCUGGUUCUUUGUUGUGGGACACCCACCUGUGGAUGAUCACCAGCUACUGGAUGAUGAUCCUUUCACUU
....((((.((((((((((....)))))).((((..((...((...---.....)).....))..)))))))).....))))((((.((((((((...)))).)))).))))........ ( -35.80)
>DroEre_CAF1 8322 100 + 1
AUUAACAGCCGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCAAA---UGUCUGGUUCUUUGUUGUGGGACACCCACUG--------------GCUACUGGAUG---AUCCUUUCACUU
......(((((..((((((....))))))..).........(((..---....))).........(((((...))))).)--------------)))...((...---..))........ ( -26.00)
>DroYak_CAF1 4371 100 + 1
GUUUACAGCCGACAACAGCGAAAGCUGUUAUCACUCCAUUCCCAAA---UAUCGUGUUCUUUGUUUUGGGACACCCACCU--------------GCUACUGGAUG---AUCCUUUCACUU
......(((.((.((((((....)))))).)).......(((((((---...((.......)).))))))).........--------------)))...((...---..))........ ( -23.90)
>DroAna_CAF1 9390 111 + 1
------GGGUGUUAAUAGCGAAAGCAGUUAUCGCUCAAUUCUGAACCAUCAUCGGGGGCUUUGUUG-GGAACACCCACCGAAAGAUGAUCGGUGGCUACUGA--GAAGAUCCUUUCACUU
------(((((.((((.((....)).)))).))))).....((((((......))((..(((.(..-(......(((((((.......)))))))...)..)--.)))..)).))))... ( -34.00)
>consensus
GUUAACAGCCGUCAACAGCGAAAGCUGUUAUCACUCCAUUCCCAAA___UACCUGGUUCUUUGUUGUGGGACACCCACCUG_GGAUGAUCACCAGCUACUGGAUGAUGAUCCUUUCACUU
......(((....((((((....))))))....................................((((.....))))................)))...((((....))))........ (-14.34 = -15.57 +   1.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:50:36 2006