Locus 1816

Sequence ID 3L_DroMel_CAF1
Location 5,100,260 – 5,100,468
Length 208
Max. P 0.906754
window2830 window2831 window2832

overview

Window 0

Location 5,100,260 – 5,100,353
Length 93
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 81.79
Mean single sequence MFE -19.14
Consensus MFE -16.16
Energy contribution -15.83
Covariance contribution -0.33
Combinations/Pair 1.19
Mean z-score -1.88
Structure conservation index 0.84
SVM decision value 1.05
SVM RNA-class probability 0.906754
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5100260 93 + 23771897
-------------GCACACAUAUACAAUGUUACCAAUACCUAGCCAAUAUGGCUGCAAUAGCGCCCUAACCUCCUCCGCCAUAUUCCAACC-CUUUUUUGGGGGGUU
-------------....((((.....))))...........(((((((((((((((....)))..............))))))))....((-((.....)))))))) ( -17.13)
>DroSec_CAF1 293333 105 + 1
CACACACACAAAUACACACAUGUACAAUGUUACCAAUACCUAGCCAAUAUGGCUGAAAUAACCCCCUAGC--CCUCCGCCAUUUUCUAGCCACCUUUUUGGGUGGUU
.................((((.....))))..........(((((.....)))))...............--...............((((((((....)))))))) ( -18.50)
>DroSim_CAF1 314944 99 + 1
------CACAAAUACACACAUGUACAAUGUUACCAAUACCUAGCCAAUAUGGCUGAAAUAGCCCCCUAGC--CCUCCGCCAUUUUCUAGCCCCCUUUUUUGGGGGUU
------...........((((.....)))).........((((.....(((((.((....((......))--..)).)))))...))))(((((......))))).. ( -21.80)
>consensus
______CACAAAUACACACAUGUACAAUGUUACCAAUACCUAGCCAAUAUGGCUGAAAUAGCCCCCUAGC__CCUCCGCCAUUUUCUAGCC_CCUUUUUGGGGGGUU
.................((((.....))))..........(((((.....)))))................................(((((((......))))))) (-16.16 = -15.83 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,100,275 – 5,100,393
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -36.48
Consensus MFE -19.59
Energy contribution -21.15
Covariance contribution 1.56
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.54
SVM decision value 0.32
SVM RNA-class probability 0.686510
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5100275 118 - 23771897
UUGCGGUUAAAUGGGCAGUGAGGGGAGGGGGGAGCACCCAAACCCCCCAAAAAAG-GGUU-GGAAUAUGGCGGAGGAGGUUAGGGCGCUAUUGCAGCCAUAUUGGCUAGGUAUUGGUAAC
((((.(.((..(((.(((((.((((.((.(((....)))...)))))).......-((((-(.(..((((((.............))))))).))))).))))).)))..)).).)))). ( -39.22)
>DroSec_CAF1 293361 111 - 1
UUGCGGUUAAAUGGGCAGUA------UGGGGGAGCUCCCAAACCACCCAAAAAGGUGGCU-AGAAAAUGGCGGAGG--GCUAGGGGGUUAUUUCAGCCAUAUUGGCUAGGUAUUGGUAAC
((((.(.((..(((.(((((------(((.(((((((((...(((((......)))))..-......((((.....--))))))))))...)))..)))))))).)))..)).).)))). ( -40.10)
>DroSim_CAF1 314966 110 - 1
UUGCGGUUAAAUGGGCAGUG-------GGAGGAAAACCCAAACCCCCAAAAAAGGGGGCU-AGAAAAUGGCGGAGG--GCUAGGGGGCUAUUUCAGCCAUAUUGGCUAGGUAUUGGUAAC
((((.(.((..(((.(((((-------((..((((.(((...(((((......)))))..-......((((.....--)))).)))....))))..)).))))).)))..)).).)))). ( -35.60)
>DroYak_CAF1 305645 101 - 1
UUGCGGUUAAAUGGGCAGUG------UGGGGAAGCU----------CCAAAAGGGGGGCUCGGAAAAUGGCGGAGG--GCUAGGG-GAUAUUUCAGCCAUAUUGGCUAGGUAUUGGUAAC
((((.(.((..(((.(((((------(((.((((((----------((......)))))........((((.....--))))...-.....)))..)))))))).)))..)).).)))). ( -31.00)
>consensus
UUGCGGUUAAAUGGGCAGUG______UGGGGGAGCACCCAAACCCCCCAAAAAGGGGGCU_AGAAAAUGGCGGAGG__GCUAGGGGGCUAUUUCAGCCAUAUUGGCUAGGUAUUGGUAAC
((((.(.((..(((.((((.......................(((((......)))))........(((((.((((..((......))..)))).))))))))).)))..)).).)))). (-19.59 = -21.15 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,100,353 – 5,100,468
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 92.04
Mean single sequence MFE -27.25
Consensus MFE -25.83
Energy contribution -25.61
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.95
SVM decision value 0.34
SVM RNA-class probability 0.697972
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5100353 115 + 23771897
UGGGUGCUCCCCCCUCCCCUCACUGCCCAUUUAACCGCAAGCCAUGCUUCUAAUGCCGCGUUGGCAUAAAUUUAAAGCAGCAGCUGCGGUUUUUCCACUGCUUUUCCUCUCUCGC
(((((...................)))))...(((((((.((..(((((...(((((.....))))).......)))))...)))))))))........................ ( -26.71)
>DroSec_CAF1 293438 109 + 1
UGGGAGCUCCCCCA------UACUGCCCAUUUAACCGCAAGCCAUGCUUCUAAUGCCGCGUUGGCAUAAAUUUAAAGCAGCAGCUGCGGUUUUUCCACUGCUUUUCCUCUCGCGC
((((......))))------....((......(((((((.((..(((((...(((((.....))))).......)))))...)))))))))........)).............. ( -27.74)
>DroSim_CAF1 315043 108 + 1
UGGGUUUUCCUCC-------CACUGCCCAUUUAACCGCAAGCCAUGCUUCUAAUGCCGCGUUGGCAUAAAUUUAAAGCAGCAGCUGCGGUUUUUCCACUGCUUUUCCUCUCUCGC
(((((........-------....)))))...(((((((.((..(((((...(((((.....))))).......)))))...)))))))))........................ ( -27.30)
>consensus
UGGGUGCUCCCCC_______CACUGCCCAUUUAACCGCAAGCCAUGCUUCUAAUGCCGCGUUGGCAUAAAUUUAAAGCAGCAGCUGCGGUUUUUCCACUGCUUUUCCUCUCUCGC
.(((....))).............((......(((((((.((..(((((...(((((.....))))).......)))))...)))))))))........)).............. (-25.83 = -25.61 +  -0.22)

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 10:17:25 2006