Locus 3560

Sequence ID 3L_DroMel_CAF1
Location 10,423,039 – 10,423,220
Length 181
Max. P 0.882783
window5551 window5552

overview

Window 1

Location 10,423,039 – 10,423,147
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.93
Mean single sequence MFE -36.07
Consensus MFE -24.21
Energy contribution -24.24
Covariance contribution 0.03
Combinations/Pair 1.17
Mean z-score -1.84
Structure conservation index 0.67
SVM decision value 0.92
SVM RNA-class probability 0.882783
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10423039 108 + 23771897
UGUGCCACUUUGACCCAGUUGGCU---CCCUAAGCGGGCUAAUGGGGAAAGGUGUAGC-C-AAACAAGCUGCCUGGUAGCCCCAGCUAUUUUUGCUGCCUUUUU-UCAU------UUUUU
..(((((((((..((((.((((((---(.......)))))))))))..)))))(((((-.-......)))))..))))....((((.......)))).......-....------..... ( -32.90)
>DroPse_CAF1 319071 107 + 1
UGUGCCACUUUGACCCAGUUGGCUGCCCCCAAAGCGGGCUAAUAGGGAAAGGUGUAGAGC-AAACAAGC-GACUGGCAGUGCCACCGAU-GCGGCUGCUGUUGC-U---------ACUUA
..(((((((((..(((.(((((((((.......)).))))))).))).))))))....))-)....(((-(((.((((((((.......-)).)))))))))))-)---------..... ( -37.60)
>DroSim_CAF1 309716 107 + 1
UGUGCCACUUUGACCCAGUUGGCU---CCCUAAGCGGGCUAAUGGGGAAAGGUGUAGC-C-AAACAAGCUGCCUGGCAGCCCCAGCCAUUUUUGCUGCCUUUUU-UCAU------UUUU-
..(((((((((..((((.((((((---(.......)))))))))))..)))))(((((-.-......)))))..))))....((((.......)))).......-....------....- ( -33.70)
>DroEre_CAF1 305275 115 + 1
UGUGCCACUUUGACCCAGUUGGCU---UCCUAAGCGGGCUAAUGGGGAAAGGUGUAGC-C-AAACAAGCUGGCUGCUAGCCACAGCCAUUUUUGCUGCCUUUUUCAUUUUUUUGUUUUUU
.((..((((((..((((.((((((---(.......)))))))))))..))))))..))-.-(((((((.((((.....))))((((.......)))).............)))))))... ( -32.90)
>DroYak_CAF1 307398 115 + 1
UGUGCCACUUUGACCCAGUUGGCU---CCCUAAGCGGGCUAAUGGGGAAAGGUGUAGC-C-AAACAAGCUGGCUGGUAGCCACAGCCAUUUUGGCUGCCUUUUUUUCAUUUUUUUUUUUU
...((((((.......)).)))).---(((.....)))..((((..((((((.(((((-(-(((.....((((((.......)))))).)))))))))))))))..)))).......... ( -40.60)
>DroAna_CAF1 299638 94 + 1
UGUGGCACUUUGACCCAGUUGGCU---CCCUAAGCGGGUUAAUGGGGAAAGGUGUAGC-CGAAACAAGCUGGUAUGCAGCCCCUGCGGCU---GCUGCUAU-------------------
.((((((((((..((((.((((((---(.......)))))))))))..)))))(((((-((......((((.....)))).....)))))---)).)))))------------------- ( -38.70)
>consensus
UGUGCCACUUUGACCCAGUUGGCU___CCCUAAGCGGGCUAAUGGGGAAAGGUGUAGC_C_AAACAAGCUGGCUGGCAGCCCCAGCCAUUUUUGCUGCCUUUUU_UCAU______UUUUU
.((..((((((..(((((((.(((........))).))))...)))..))))))..))................((((((.............))))))..................... (-24.21 = -24.24 +   0.03)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 10,423,114 – 10,423,220
Length 106
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 77.89
Mean single sequence MFE -28.55
Consensus MFE -16.87
Energy contribution -17.82
Covariance contribution 0.95
Combinations/Pair 1.13
Mean z-score -1.53
Structure conservation index 0.59
SVM decision value 0.11
SVM RNA-class probability 0.587369
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10423114 106 + 23771897
CCCAGCUAUUUUUGCUGCCUUUUU-UCAU------UUUUUCUUUCAAUGCCGUAGUUGAUGCUGAAGUUUCGGUAGUUGAGUAGCAGUAGCAGUAGCUUUAAGCUGGGGGGCA
(((((((.....((((((..(((.-.(..------........(((((......)))))((((((....)))))))..)))..))))))((....))....)))))))..... ( -31.10)
>DroSec_CAF1 294084 99 + 1
CCCAGCCAUUUUUGCUGCCUUUUU-UCAU------UUUUUUUUUCAAUGCCGUAGUUGAUGCUGAAGUUUCGGUAGUUGAGUAGC------AGUAGCUCUAUGCUGGG-GGCA
((((((.....(((((((..(((.-.(..------........(((((......)))))((((((....)))))))..)))..))------)))))......))))))-.... ( -28.70)
>DroSim_CAF1 309791 98 + 1
CCCAGCCAUUUUUGCUGCCUUUUU-UCAU------UUUU-UUUUCAAUGCCGUAGUUGAUGCUGAAGUUUCGGUAGUUGAGUAGC------AGUAGCUCUAAGCUGGA-GGCA
.(((((.....(((((((..(((.-.(..------....-...(((((......)))))((((((....)))))))..)))..))------)))))......))))).-.... ( -25.50)
>DroEre_CAF1 305350 106 + 1
CACAGCCAUUUUUGCUGCCUUUUUCAUUUUUUUGUUUUUUUUUUCAAUGCCGUAGUUGAUGCUGAAGUUUCGGUAGUUGAGUAGC------AGUAGCUCUAAGCUGGG-GGCA
....(((....(((((((.........................(((((......)))))((((((....)))))).....)))))------))((((.....))))..-))). ( -24.40)
>DroYak_CAF1 307473 112 + 1
CACAGCCAUUUUGGCUGCCUUUUUUUCAUUUUUUUUUUUUUUUUCAAUGCCGUAGUUGAUGCUGAAGUUUCGGUAGUUGAGUAGCAGUAGCAGUAGCUCUAAGCUGGG-GGCA
...((((.....))))(((((.....................((((((((((((((....))))......))))).)))))((((((.(((....)))))..))))))-))). ( -26.40)
>DroAna_CAF1 299714 89 + 1
CCCUGCGGCU---GCUGCUAU-------------------UUUCAGAUGCUGUACUUGAUGCCAAAGUUGCAGUAGUCGAGUGGCAGUGGCAGUAGCACUA-GCCGCG-AGCU
...(((((((---(.((((((-------------------(.(((..((((..(((((((((.......)))....)))))))))).))).))))))).))-))))))-.... ( -35.20)
>consensus
CCCAGCCAUUUUUGCUGCCUUUUU_UCAU______UUUUUUUUUCAAUGCCGUAGUUGAUGCUGAAGUUUCGGUAGUUGAGUAGC______AGUAGCUCUAAGCUGGG_GGCA
....(((......(((((.........................(((((......)))))((((((....)))))).....)))))........((((.....))))...))). (-16.87 = -17.82 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:00 2006