Locus 3143

Sequence ID 3L_DroMel_CAF1
Location 9,147,474 – 9,147,602
Length 128
Max. P 0.883864
window4903 window4904

overview

Window 3

Location 9,147,474 – 9,147,568
Length 94
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 91.82
Mean single sequence MFE -28.52
Consensus MFE -24.89
Energy contribution -25.25
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.87
SVM decision value 0.93
SVM RNA-class probability 0.883864
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9147474 94 + 23771897
AACCGAGCCCAAAACGUGUCGCCUCAAGUGCCACGCCAUCUUAUCGCUGGCCACAGUUUGUUGCCUUAUCUUGAGGCACUGCACGUUUGCCACA----
....(.((...((((((((.((((((((......((.........)).(((.((.....)).)))....))))))))...)))))))))))...---- ( -28.00)
>DroPse_CAF1 2676 94 + 1
AGCCAAGCCAAAAACGUGUCGCCUCAAGUGCCACGCCAUCUUAUCGCUGCCCACAGUUUGUUGCCUUAUCUUGAGGCACUGCACGUUUACGGCU----
.....((((..((((((((.((((((((......((...(.....((((....))))..)..)).....))))))))...))))))))..))))---- ( -30.20)
>DroSec_CAF1 2565 94 + 1
AACCGAGCCCAAAACGUGUCGCCCCAAGUGCCACGCCAUCUUAUCGCUGGCCACAGUUUGUUGCCUUAUCUUGAGGCACUGCACGUUUGCCACA----
....(.((...((((((((.(......((((((.((.........))))).))).......((((((.....))))))).)))))))))))...---- ( -24.30)
>DroEre_CAF1 14559 98 + 1
AGCCGAGCCCAAAACGUGUCGCCUCAAGUGCCACGCCAUCUUAUCGCUGGCCACAGUUUGUUGCCUUAUCUUGAGGCACUGCACGUUUGCCGCACACA
......((...((((((((.((((((((......((.........)).(((.((.....)).)))....))))))))...))))))))...))..... ( -30.50)
>DroAna_CAF1 2689 94 + 1
AGCCAAGCCCAAAACGUGUCGCCUCAAGUGCCACGCCAUCUUAUCGCUGCCCACAGUUUGUUGCCUUAUCUUGAGGCGCUGCACGUUUGUAGUG----
......((...(((((((((((((((((......((...(.....((((....))))..)..)).....)))))))))..))))))))...)).---- ( -27.90)
>DroPer_CAF1 2665 94 + 1
AGCCAAGCCAAAAACGUGUCGCCUCAAGUGCCACGCCAUCUUAUCGCUGCCCACAGUUUGUUGCCUUAUCUUGAGGCAGUGCACGUUUACGGCU----
.....((((..((((((((.((((((((......((...(.....((((....))))..)..)).....))))))))...))))))))..))))---- ( -30.20)
>consensus
AGCCAAGCCCAAAACGUGUCGCCUCAAGUGCCACGCCAUCUUAUCGCUGCCCACAGUUUGUUGCCUUAUCUUGAGGCACUGCACGUUUGCCGCA____
......((...((((((((.((((((((......((...(.....((((....))))..)..)).....))))))))...))))))))...))..... (-24.89 = -25.25 +   0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,147,507 – 9,147,602
Length 95
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 76.69
Mean single sequence MFE -24.63
Consensus MFE -14.29
Energy contribution -14.40
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.58
SVM decision value 0.34
SVM RNA-class probability 0.694631
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9147507 95 - 23771897
UGUACAUACAUAUAUACACACCUCUAUAUAUGU--G--------UGUGGCAAACGUGCAGUGCCUCAAGAUAAGGCAACAAACUGUGGCCAGCGAUAAGAUGGCG
((((((((((((((((........)))))))))--)--------))).))).....(((((((((.......)))).....))))).((((.(.....).)))). ( -28.80)
>DroPse_CAF1 2709 75 - 1
---------------ACACACAUUCGAA-------G--------AGCCGUAAACGUGCAGUGCCUCAAGAUAAGGCAACAAACUGUGGGCAGCGAUAAGAUGGCG
---------------.............-------.--------.(((((.....(((..((((.((......(....)......))))))))).....))))). ( -18.60)
>DroSec_CAF1 2598 95 - 1
UGUACAUACAUAUAUACACACCUCUAUAUAUGU--G--------UGUGGCAAACGUGCAGUGCCUCAAGAUAAGGCAACAAACUGUGGCCAGCGAUAAGAUGGCG
((((((((((((((((........)))))))))--)--------))).))).....(((((((((.......)))).....))))).((((.(.....).)))). ( -28.80)
>DroEre_CAF1 14592 87 - 1
----------------CACACCUCUGUAUAUGU--GUGUGUGUGUGCGGCAAACGUGCAGUGCCUCAAGAUAAGGCAACAAACUGUGGCCAGCGAUAAGAUGGCG
----------------((((...(((((((..(--....)..))))))).....((....(((((.......)))))....))))))((((.(.....).)))). ( -23.70)
>DroYak_CAF1 15735 94 - 1
-----------ACAUACACACCUCUAUAUAUGUGUGUGUGUGUGUGUGGCAAACGUGCAGUGCCUCAAGAUAAGGCAACAAACUGUGGCCAGCGAUAAGAUGGCG
-----------(((((((((((.(.......).).)))))))))).((((....((....(((((.......)))))....))....))))((.((...)).)). ( -28.80)
>DroPer_CAF1 2698 75 - 1
---------------ACACACAUUCGAA-------G--------AGCCGUAAACGUGCACUGCCUCAAGAUAAGGCAACAAACUGUGGGCAGCGAUAAGAUGGCG
---------------.............-------.--------.(((((.......(.(((((.((......(....)......))))))).).....))))). ( -19.10)
>consensus
_______________ACACACCUCUAUAUAUGU__G________UGCGGCAAACGUGCAGUGCCUCAAGAUAAGGCAACAAACUGUGGCCAGCGAUAAGAUGGCG
................((((............................(((....)))..(((((.......)))))......))))((((.(.....).)))). (-14.29 = -14.40 +   0.11)

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 10:50:38 2006