Locus 3400

Sequence ID 2L_DroMel_CAF1
Location 9,844,479 – 9,844,614
Length 135
Max. P 0.943510
window5380 window5381 window5382

overview

Window 0

Location 9,844,479 – 9,844,581
Length 102
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 82.31
Mean single sequence MFE -27.90
Consensus MFE -16.05
Energy contribution -17.61
Covariance contribution 1.56
Combinations/Pair 1.08
Mean z-score -2.71
Structure conservation index 0.58
SVM decision value 0.46
SVM RNA-class probability 0.745924
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9844479 102 + 22407834
CGGCUUCUG---CCAUC--UCAACUGUGCUGUUACUGACUUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCA
........(---(((((--.....((((.((.((((...((((((((.........))))))))...)))).)).))))....(((....)))......)))))).. ( -30.60)
>DroPse_CAF1 56358 89 + 1
--GCUGCUG---C-------------UGCUGCCGCCGGCUUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUCCGCUUCCACCUUAAUUGAUGGCCA
--((.((..---.-------------.)).)).((((((((.(((((.........))))))))))..(((....)))........................))).. ( -24.60)
>DroSim_CAF1 56204 104 + 1
CGGCUUCUG---CCAUCUUUCAACUGUGCUGUUGCUGACUUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCA
........(---(((((....(((......)))(((((..(((((((.........)))))))(((((((.........))))))).))))).......)))))).. ( -31.50)
>DroYak_CAF1 55971 102 + 1
CGGCUUCUG---CCAUC--UCAACUGCGCUGUUGCUGACUUUGAUGCCUUCACUUAGCUUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCA
........(---(((((--......(.((((..((..(..(((.((....(((((.((.....)).)))))....))))).)..))..)))))......)))))).. ( -30.00)
>DroAna_CAF1 59816 90 + 1
---C------------C--UCCGCAAUGCUGUUGCUGACUUUGAUGCCUUUACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCA
---.------------.--.(((((((......(((((..(((((((.........)))))))(((((((.........))))))).)))))....)))).)))... ( -25.70)
>DroPer_CAF1 56857 92 + 1
--GCUGCUGCUGC-------------UGCUGCCGCCGGCUUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUCCGCUUCCACCUUAAUUGAUGGCCA
--((.((....))-------------.))....((((((((.(((((.........))))))))))..(((....)))........................))).. ( -25.00)
>consensus
__GCUUCUG___C___C__UCAACUGUGCUGUUGCUGACUUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCA
...........................(((((((((((..(((((((.........)))))))(((((((.........))))))).))))).......)))))).. (-16.05 = -17.61 +   1.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,844,479 – 9,844,581
Length 102
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 82.31
Mean single sequence MFE -36.02
Consensus MFE -23.04
Energy contribution -22.98
Covariance contribution -0.05
Combinations/Pair 1.22
Mean z-score -3.82
Structure conservation index 0.64
SVM decision value 1.34
SVM RNA-class probability 0.943510
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9844479 102 - 22407834
UGGCCAUCAAUUAAGGCUGAAGCCAAAUUGUGUUGACACUUGGCUUGAUGCUAAGUGAAGGCAUCAAAGUCAGUAACAGCACAGUUGA--GAUGG---CAGAAGCCG
..((((((......(((....))).((((((((((..(((.(((((((((((.......)))))).))))))))..))))))))))..--)))))---)........ ( -42.50)
>DroPse_CAF1 56358 89 - 1
UGGCCAUCAAUUAAGGUGGAAGCGGAAUUGUGUUGACACUUGGCUUGAUGCUAAGUGAAGGCAUCAAAGCCGGCGGCAGCA-------------G---CAGCAGC--
...(((((......)))))...(((..(((((((..((((((((.....))))))))..)))).)))..)))((.((....-------------)---).))...-- ( -31.80)
>DroSim_CAF1 56204 104 - 1
UGGCCAUCAAUUAAGGCUGAAGCCAAAUUGUGUUGACACUUGGCUUGAUGCUAAGUGAAGGCAUCAAAGUCAGCAACAGCACAGUUGAAAGAUGG---CAGAAGCCG
..((((((......(((....))).((((((((((.((((((((.....))))))))..(((......))).....))))))))))....)))))---)........ ( -41.80)
>DroYak_CAF1 55971 102 - 1
UGGCCAUCAAUUAAGGCUGAAGCCAAAUUGUGUUGACACUUGGCUUGAAGCUAAGUGAAGGCAUCAAAGUCAGCAACAGCGCAGUUGA--GAUGG---CAGAAGCCG
..((((((......(((....))).((((((((((.((((((((.....))))))))..(((......))).....))))))))))..--)))))---)........ ( -41.10)
>DroAna_CAF1 59816 90 - 1
UGGCCAUCAAUUAAGGCUGAAGCCAAAUUGUGUUGACACUUGGCUUGAUGCUAAGUAAAGGCAUCAAAGUCAGCAACAGCAUUGCGGA--G------------G---
...((..((((....(((((.(((((...(((....))))))))((((((((.......))))))))..)))))......)))).)).--.------------.--- ( -26.40)
>DroPer_CAF1 56857 92 - 1
UGGCCAUCAAUUAAGGUGGAAGCGGAAUUGUGUUGACACUUGGCUUGAUGCUAAGUGAAGGCAUCAAAGCCGGCGGCAGCA-------------GCAGCAGCAGC--
...(((((......)))))..((((..(((((((..((((((((.....))))))))..)))).)))..)).((.((....-------------)).)).))...-- ( -32.50)
>consensus
UGGCCAUCAAUUAAGGCUGAAGCCAAAUUGUGUUGACACUUGGCUUGAUGCUAAGUGAAGGCAUCAAAGUCAGCAACAGCACAGUUGA__G___G___CAGAAGC__
.((((.........))))...........((((((....(((((((((((((.......)))))).)))))))...))))))......................... (-23.04 = -22.98 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,844,513 – 9,844,614
Length 101
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 85.23
Mean single sequence MFE -19.33
Consensus MFE -14.87
Energy contribution -15.70
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.77
SVM decision value 0.07
SVM RNA-class probability 0.570279
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9844513 101 + 22407834
UUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCAUAAUGCACACACACACACAACUCUUCAC---CGGCG----
.(((((((.........)))))))(((..(((....)))....(((((((((......)))).)))))............................---.))).---- ( -23.40)
>DroPse_CAF1 56379 100 + 1
UUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUCCGCUUCCACCUUAAUUGAUGGCCAUAAUGCACA--------CAGCUCUGCUUACCCUUCAAGCC
.(((((((.........)))))))((...(((....)))...................((((.((...(((.(((..--------......)))))).)).)))))). ( -15.80)
>DroEre_CAF1 55807 95 + 1
UUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCAUAAUGCACA------CACAACUCUUCCC---CUCCG----
.(((((((.........)))))))((((.((....)).(((((.(((....)))..))))).))))...........------.............---.....---- ( -20.20)
>DroYak_CAF1 56005 91 + 1
UUUGAUGCCUUCACUUAGCUUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCAUAAUGCA----------CAACUCUUCCC---CUGCG----
......(((.(((.((((((..(((((((((.........))))))))).)))..))).))).)))......(((----------...........---.))).---- ( -20.60)
>DroAna_CAF1 59838 96 + 1
UUUGAUGCCUUUACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCAUAAUGCAC--------ACAACUCUUCUUAC-CUGCC---C
.(((((((.........)))))))((((.((....)).(((((.(((....)))..))))).))))..........--------..............-.....---. ( -20.20)
>DroPer_CAF1 56881 100 + 1
UUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUCCGCUUCCACCUUAAUUGAUGGCCAUAAUGCACA--------CAGCUCUGCUUACCCUUCAAGCC
.(((((((.........)))))))((...(((....)))...................((((.((...(((.(((..--------......)))))).)).)))))). ( -15.80)
>consensus
UUUGAUGCCUUCACUUAGCAUCAAGCCAAGUGUCAACACAAUUUGGCUUCAGCCUUAAUUGAUGGCCAUAAUGCACA________CAACUCUUCUC___CUGCG____
.(((((((.........)))))))((((.((....)).(((((.(((....)))..))))).)))).......................................... (-14.87 = -15.70 +   0.83)

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 10:51:34 2006