Locus 1477

Sequence ID 3R_DroMel_CAF1
Location 4,264,473 – 4,264,596
Length 123
Max. P 0.727084
window2453 window2454 window2455

overview

Window 3

Location 4,264,473 – 4,264,564
Length 91
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 75.66
Mean single sequence MFE -32.38
Consensus MFE -17.52
Energy contribution -19.28
Covariance contribution 1.76
Combinations/Pair 1.15
Mean z-score -1.67
Structure conservation index 0.54
SVM decision value -0.05
SVM RNA-class probability 0.508522
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4264473 91 + 27905053
GUAGGGGCAG------------------GAGGCC-ACGGGCCGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCUCUCUCGGACCGGAUUUUGUUUGCCUGACUUUGU
((..((((((------------------(.((((-...))))(((((((((.(((....)))(((((.........)))))....))))))))).))))))).))..... ( -33.10)
>DroSec_CAF1 66172 92 + 1
GUAGGGGCAG------------------GAGGCCCCCGGGCAGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCUCUCUCGGACCGGAUUUUGUUUGCCUGACUUUGU
...(((((..------------------...)))))(((((((((((((((.(((....)))(((((.........)))))....))))))))...)))))))....... ( -37.10)
>DroSim_CAF1 66035 90 + 1
GUAGGGGUAG------------------GAGGCCCCCGGGCAGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCU--CUCGGACCGGAUUUUGUUUGCCUGACUUUGU
...(((((..------------------...)))))(((((((((((((((.(((....))).((((.........)--)))...))))))))...)))))))....... ( -35.30)
>DroEre_CAF1 69074 106 + 1
GGACGAG-AGCUGCAGCUGGAGAACCUGAAGG-CCCCGGGCAGGAGUCCGGAGUCAAUAGAGAGAGAUAUAUCUCCU--CUCGGACCGGAUUUUGUUUGCCUGACUUUGU
..(((((-.(((....(.((....)).)..))-)..(((((((((((((((..((...((((.((((....))))))--))..))))))))))...)))))))..))))) ( -34.30)
>DroAna_CAF1 68825 78 + 1
CUAGGCGAAA------------------GAAGUCUU-------UAGCUUGCAGUCCAUAGACAGAGAUAUAUCUC-------UGGUCGGAUUUUGUUUGGCUGACUUUGU
..........------------------((((((..-------.((((.(((((((.....((((((....))))-------))...))))..)))..)))))))))).. ( -22.10)
>consensus
GUAGGGGCAG__________________GAGGCCCCCGGGCAGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCU__CUCGGACCGGAUUUUGUUUGCCUGACUUUGU
............................((((....(((((((((((((((.(((....))).((((....))))..........)))))))))...)))))).)))).. (-17.52 = -19.28 +   1.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,264,486 – 4,264,596
Length 110
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 82.48
Mean single sequence MFE -36.10
Consensus MFE -20.50
Energy contribution -20.83
Covariance contribution 0.33
Combinations/Pair 1.08
Mean z-score -2.77
Structure conservation index 0.57
SVM decision value 0.41
SVM RNA-class probability 0.727084
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4264486 110 + 27905053
GCC-ACGGGCCGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCUCUCUCGGACCGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCCGGA
.((-..((((((((((((((.(((....)))(((((.........)))))....))))))))))...))))(((...(((((((.(((....))))))))))..))).)). ( -40.50)
>DroPse_CAF1 74101 84 + 1
---------CCGGA----GGAGUCUAUAGAUA--CAUAUAUCUGCU---------CGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCU---
---------..((.----(((((((.((((((--....))))))..---------.))))))).....)).(((...(((((((.(((....))))))))))..))).--- ( -22.90)
>DroSec_CAF1 66185 111 + 1
GCCCCCGGGCAGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCUCUCUCGGACCGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCUGGA
....((((((((((((((((.(((....)))(((((.........)))))....)))))))....(((((.....((((((.(....).)))))).)))))))))))))). ( -42.90)
>DroEre_CAF1 69104 108 + 1
G-CCCCGGGCAGGAGUCCGGAGUCAAUAGAGAGAGAUAUAUCUCCU--CUCGGACCGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCCGGA
.-..((((((((((((((((..((...((((.((((....))))))--))..)))))))))....(((((.....((((((.(....).)))))).)))))))))))))). ( -47.80)
>DroYak_CAF1 68034 108 + 1
G-CCCCGAGCAGGAGUCCGAAGUCAAUAGACAGAGAUAUAUCUUCU--CUCGGACCGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCCGGA
.-..(((..((((.((((((.(((....))).((((.......)))--)))))))..........(((((.....((((((.(....).)))))).)))))))))..))). ( -39.60)
>DroPer_CAF1 74563 84 + 1
---------CCGGA----GGAGUCUAUAGAUA--CAUAUAUCUGCU---------CGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCU---
---------..((.----(((((((.((((((--....))))))..---------.))))))).....)).(((...(((((((.(((....))))))))))..))).--- ( -22.90)
>consensus
G_C_CCGGGCAGGAGUCCGGAGUCAAUAGACAGAGAUAUAUCUCCU__CUCGGACCGGAUUUUGUUUGCCUGACUUUGUUGCCACUUGCCAACAAUGGCAACCUGUCCGGA
..................((((...(((........)))..)))).........((((((...(.(((((.....((((((.(....).)))))).))))).).)))))). (-20.50 = -20.83 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,264,486 – 4,264,596
Length 110
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 82.48
Mean single sequence MFE -33.77
Consensus MFE -21.61
Energy contribution -22.28
Covariance contribution 0.67
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.64
SVM decision value 0.18
SVM RNA-class probability 0.622626
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4264486 110 - 27905053
UCCGGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCGGUCCGAGAGAGGAGAUAUAUCUCUGUCUAUUGACUCCGGACUCCGGCCCGU-GGC
.((.(((..(((((((((.......)))))))))...))).))....((....((((((((.(((.(((((....))))).((....)))))))))..))))....)-).. ( -38.30)
>DroPse_CAF1 74101 84 - 1
---AGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCG---------AGCAGAUAUAUG--UAUCUAUAGACUCC----UCCGG---------
---.(((..(((((((((.......)))))))))...))).............(((---------((.((.((((..--....))))..)).)----).)))--------- ( -21.10)
>DroSec_CAF1 66185 111 - 1
UCCAGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCGGUCCGAGAGAGGAGAUAUAUCUCUGUCUAUUGACUCCGGACUCCUGCCCGGGGGC
(((.(((..(((((((((.......)))))))))...))).((((.......(((((..(((.((((((((....))))).))).)))...)))))....)))).)))... ( -39.40)
>DroEre_CAF1 69104 108 - 1
UCCGGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCGGUCCGAG--AGGAGAUAUAUCUCUCUCUAUUGACUCCGGACUCCUGCCCGGGG-C
(((((.(((((((((.((((((.(....).)))))).....)))))......(((((((..((--((((((....)))).))))...))..)))))..)))).))))).-. ( -42.60)
>DroYak_CAF1 68034 108 - 1
UCCGGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCGGUCCGAG--AGAAGAUAUAUCUCUGUCUAUUGACUUCGGACUCCUGCUCGGGG-C
((((..(((((((((.((((((.(....).)))))).....))))).........((((((((--(((.......)))).(((....))).)))))))))))..)))).-. ( -40.10)
>DroPer_CAF1 74563 84 - 1
---AGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCG---------AGCAGAUAUAUG--UAUCUAUAGACUCC----UCCGG---------
---.(((..(((((((((.......)))))))))...))).............(((---------((.((.((((..--....))))..)).)----).)))--------- ( -21.10)
>consensus
UCCAGACAGGUUGCCAUUGUUGGCAAGUGGCAACAAAGUCAGGCAAACAAAAUCCGGUCCGAG__AGGAGAUAUAUCUCUGUCUAUUGACUCCGGACUCCGGCCCGG_G_C
....(((..(((((((((.......)))))))))...)))...............((((((.......(((((......)))))........))))))............. (-21.61 = -22.28 +   0.67)

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 10:11:32 2006