Locus 1697

Sequence ID 2L_DroMel_CAF1
Location 4,641,806 – 4,642,028
Length 222
Max. P 0.999297
window2714 window2715 window2716 window2717 window2718

overview

Window 4

Location 4,641,806 – 4,641,911
Length 105
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 72.86
Mean single sequence MFE -34.35
Consensus MFE -18.93
Energy contribution -20.27
Covariance contribution 1.34
Combinations/Pair 1.10
Mean z-score -2.94
Structure conservation index 0.55
SVM decision value 3.49
SVM RNA-class probability 0.999297
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641806 105 + 22407834
AAUUUCCAGGAUUACUGGGAUCAACGGGCUCGGGUCCAUCGGGAAUACCAAAUCUUCCCGG------------GACAAAUGCCUCUCCAGGUUGGAGUUCACCUGGAUCUUCGAUUC
.....((((.....))))((((...((((....((((..((((((.........)))))))------------)))....)))).(((((((........))))))).....)))). ( -37.50)
>DroSec_CAF1 78834 105 + 1
AACCUCCAGGAUUAAUAGGACCAACAGUCUCGAGUCCAUCGGGAAUUCCAAAUCUUCCCGG------------GACACACGUCUCUCCAGGUUGGAGUUCUCCUGGAUCUUCGAUUC
....(((((((......(((((.........).)))).....(((((((((.(((....((------------(((....)))))...))))))))))))))))))).......... ( -32.90)
>DroYak_CAF1 83719 117 + 1
AACCUCCAGGAAUACAAGGACCACCUGGCUCCAUUGCAUUGGGACCACCAUAUCCUCCCCAACAAUCUCCUAUAACAUCUGCAACGCCAGGUUGGAGUUCUCCUGGAAUUUCGAUUC
....(((((((..((.....(((((((((....((((((((((..............))))).................))))).)))))).))).))..))))))).......... ( -32.66)
>consensus
AACCUCCAGGAUUACUAGGACCAACAGGCUCGAGUCCAUCGGGAAUACCAAAUCUUCCCGG____________GACAAAUGCCUCUCCAGGUUGGAGUUCUCCUGGAUCUUCGAUUC
....((((((.......((((............)))).(((((((.........))))))).......................((((.....))))....)))))).......... (-18.93 = -20.27 +   1.34)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,641,806 – 4,641,911
Length 105
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 72.86
Mean single sequence MFE -37.00
Consensus MFE -21.35
Energy contribution -22.47
Covariance contribution 1.12
Combinations/Pair 1.13
Mean z-score -1.89
Structure conservation index 0.58
SVM decision value 1.13
SVM RNA-class probability 0.919946
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641806 105 - 22407834
GAAUCGAAGAUCCAGGUGAACUCCAACCUGGAGAGGCAUUUGUC------------CCGGGAAGAUUUGGUAUUCCCGAUGGACCCGAGCCCGUUGAUCCCAGUAAUCCUGGAAAUU
..(((((...(((((((........)))))))(.(((....(((------------(((((((.........))))))..))))....)))).))))).((((.....))))..... ( -36.00)
>DroSec_CAF1 78834 105 - 1
GAAUCGAAGAUCCAGGAGAACUCCAACCUGGAGAGACGUGUGUC------------CCGGGAAGAUUUGGAAUUCCCGAUGGACUCGAGACUGUUGGUCCUAUUAAUCCUGGAGGUU
..........(((((((...((((.....))))...((...(((------------(((((((.........))))))..)))).)).(((.....))).......))))))).... ( -34.00)
>DroYak_CAF1 83719 117 - 1
GAAUCGAAAUUCCAGGAGAACUCCAACCUGGCGUUGCAGAUGUUAUAGGAGAUUGUUGGGGAGGAUAUGGUGGUCCCAAUGCAAUGGAGCCAGGUGGUCCUUGUAUUCCUGGAGGUU
.........(((((((((.((.(((.(((((((((((.(((.((....)).)))(((((((..(......)..))))))))))))...))))))))).....)).)))))))))... ( -41.00)
>consensus
GAAUCGAAGAUCCAGGAGAACUCCAACCUGGAGAGGCAUAUGUC____________CCGGGAAGAUUUGGUAUUCCCGAUGGACUCGAGCCAGUUGGUCCUAGUAAUCCUGGAGGUU
..........(((((((...((((.....)))).........................((((......((....))((((((........)))))).)))).....))))))).... (-21.35 = -22.47 +   1.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,641,846 – 4,641,951
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 63.88
Mean single sequence MFE -27.62
Consensus MFE -11.10
Energy contribution -14.16
Covariance contribution 3.06
Combinations/Pair 1.10
Mean z-score -2.12
Structure conservation index 0.40
SVM decision value 0.36
SVM RNA-class probability 0.704237
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641846 105 + 22407834
GGGAAUACCAAAU---CUUCCCGG------------GACAAAUGCCUCUCCAGGUUGGAGUUCACCUGGAUCUUCGAUUCCUUCCUACCAACUGCCAGGAAUACAACAGCAACCAGGCUC
(((((........---.)))))..------------.......((((.(((((((........)))))))......((((((..(........)..))))))............)))).. ( -25.80)
>DroSec_CAF1 78874 105 + 1
GGGAAUUCCAAAU---CUUCCCGG------------GACACACGUCUCUCCAGGUUGGAGUUCUCCUGGAUCUUCGAUUCCUUCCGACCAACUUCCAGGAAUACAACUGCAACCAGGCUC
(((((........---.)))))((------------(((....))))).((.(((((.((((.(((((((...(((........)))......)))))))....)))).))))).))... ( -35.50)
>DroEre_CAF1 84000 96 + 1
--------UAUGCCUGCCUCUCCACCC--------------AUACA--ACCAGGUUGGAGUCCACCUGGAUCACCUUCUCCUCCCUUCCCACCGCCAGGACUACCGGAAACACCAGGUUG
--------...(((((....(((....--------------.....--.((((((.((...)))))))).........((((..(........)..)))).....))).....))))).. ( -21.60)
>DroYak_CAF1 83759 117 + 1
GGGACCACCAUAU---CCUCCCCAACAAUCUCCUAUAACAUCUGCAACGCCAGGUUGGAGUUCUCCUGGAAUUUCGAUUCCUUCCUUCCAACACCCAGGGCUACAACAGCCACCAGGCGC
((((.........---..)))).........................((((..(((((((.......(((((....)))))....)))))))......((((.....))))....)))). ( -27.60)
>consensus
GGGAAUACCAAAU___CCUCCCCA____________GACA_AUGCAUCUCCAGGUUGGAGUUCACCUGGAUCUUCGAUUCCUUCCUACCAACUGCCAGGAAUACAACAGCAACCAGGCUC
(((((............)))))..........................(((.(((((..((..((((((.........................))))))..)).....))))).))).. (-11.10 = -14.16 +   3.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,641,871 – 4,641,991
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 63.33
Mean single sequence MFE -27.87
Consensus MFE -13.53
Energy contribution -13.54
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.64
Structure conservation index 0.49
SVM decision value 0.29
SVM RNA-class probability 0.672278
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641871 120 + 22407834
AAUGCCUCUCCAGGUUGGAGUUCACCUGGAUCUUCGAUUCCUUCCUACCAACUGCCAGGAAUACAACAGCAACCAGGCUCAAGUCCAGUAGAAUAUCCACAUGCUCCUAUCAAACCUCCA
...........((((((((((.....(((((.(((.((((((..(........)..)))))).........((..(((....)))..)).))).)))))...))))).....)))))... ( -24.60)
>DroSec_CAF1 78899 104 + 1
CACGUCUCUCCAGGUUGGAGUUCUCCUGGAUCUUCGAUUCCUUCCGACCAACUUCCAGGAAUACAACUGCAACCAGGCUCAAGUUCUG------GUCCUCAAG----------UCCUCCA
............(((((.((((.(((((((...(((........)))......)))))))....)))).)))))(((..((.....))------..)))....----------....... ( -26.40)
>DroEre_CAF1 84019 117 + 1
-AUACA--ACCAGGUUGGAGUCCACCUGGAUCACCUUCUCCUCCCUUCCCACCGCCAGGACUACCGGAAACACCAGGUUGGAAUCCAUGGGGGUCUGAGAAUCGUCCCAUCCAUCCUCCG
-.....--...(((.((((((((....))))....((((((((((((((.(((....((....))(....)....))).)))).....)))))...)))))........)))).)))... ( -32.60)
>consensus
_AUGCCUCUCCAGGUUGGAGUUCACCUGGAUCUUCGAUUCCUUCCUACCAACUGCCAGGAAUACAACAGCAACCAGGCUCAAGUCCAG__G__UAUCCACAUG_UCC_AUC_AUCCUCCA
................(((.((..(((((.......((((((..............))))))..........)))))...)).))).................................. (-13.53 = -13.54 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,641,911 – 4,642,028
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 57.42
Mean single sequence MFE -30.51
Consensus MFE -12.58
Energy contribution -11.81
Covariance contribution -0.77
Combinations/Pair 1.29
Mean z-score -2.12
Structure conservation index 0.41
SVM decision value 1.19
SVM RNA-class probability 0.928076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4641911 117 + 22407834
CUUCCUACCAACUGCCAGGAAUACAACAGCAACCAGGCUCAAGUCCAGUAGAAUAUCCACAUGCUCCUAUCAAACCUCCAA---GUUCCGCCCCGGCAGGUUGGAGCUCACCAGGAUCAC
..((((.....((((..(((.......(((......)))....))).))))...........(((((.....(((((((..---..........)).)))))))))).....)))).... ( -25.00)
>DroSec_CAF1 78939 93 + 1
CUUCCGACCAACUUCCAGGAAUACAACUGCAACCAGGCUCAAGUUCUG------GUCCUCAAG----------UCCUCCAA---CCUC--------AAGGUUGGAGUCCACCUGGAACUU
............(((((((............(((((((....).))))------))......(----------..((((((---((..--------..))))))))..).)))))))... ( -32.40)
>DroEre_CAF1 84056 120 + 1
CUCCCUUCCCACCGCCAGGACUACCGGAAACACCAGGUUGGAAUCCAUGGGGGUCUGAGAAUCGUCCCAUCCAUCCUCCGGCGCAUCCCGUACCACCCGGUUGGAGUUCACCUGGAUCAC
...........((....))......(....).((((((.(((.(((((((((((.((.((..((((.............))))..)).)).))).))))..)))).)))))))))..... ( -34.12)
>consensus
CUUCCUACCAACUGCCAGGAAUACAACAGCAACCAGGCUCAAGUCCAG__G__UAUCCACAUG_UCC_AUC_AUCCUCCAA___AUUCCG__CC__CAGGUUGGAGUUCACCUGGAUCAC
..............(((((................(((....)))..............................((((((...................))))))....)))))..... (-12.58 = -11.81 +  -0.77)

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 10:08:45 2006