Locus 3028

Sequence ID	3L_DroMel_CAF1
Location	8,691,829 – 8,691,923
Length	94
Max. P	0.866330

overview

Window 2

Location	8,691,829 – 8,691,923
Length	94
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	87.37
Mean single sequence MFE	-34.86
Consensus MFE	-28.40
Energy contribution	-28.36
Covariance contribution	-0.04
Combinations/Pair	1.10
Mean z-score	-1.70
Structure conservation index	0.81
SVM decision value	0.59
SVM RNA-class probability	0.792550
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8691829 94 + 23771897
AACAUCAAUCCGCUGCGAGUGGCCACCAACGAAGCUGGCCAGUUAACAACCACUUCCAGCGCCGAUGGCAGCUGCCAGGCGAGGAUCUGGGGAU--------
.......((((.....((.((((((.(......).)))))).)).....(((..(((..((((..((((....)))))))).)))..)))))))-------- ( -35.30)
>DroSec_CAF1 79679 94 + 1
AUCAUCAAUCCGCUGCGAGUGGCCACCAACGUAGCUGGCCGGUUAACAACCACUUCCAGCGCCGAUGGCAGCUGCCAGGCGAGGAUCUGGGGAU--------
(((..((((((((((.(((((((((.(......).)))))(((.....))))))).))))(((..((((....)))))))..)))).))..)))-------- ( -38.30)
>DroSim_CAF1 80185 94 + 1
AUCAUCAAUCCACUGCGAGUGGCCACCAACGAAGCUGGCCAGUUAACAACCACUUCCAGCGCCGAUGUCAGCUGCCAGGCGAGGAUCUGGGGAU--------
.......((((.....((.((((((.(......).)))))).)).....(((..(((..((((...((.....))..)))).)))..)))))))-------- ( -29.30)
>DroEre_CAF1 84279 99 + 1
AUCAUCAAUCCGCCGCAAGUGGCCACCAACGAAGCUGGCCAGUUAC---CCACUUCCAGCAUCGAUGGCAGCUGCCAGGCGAGGAACUGAGGAUCAGGAGGA
.((.((..(((..(((..(..((..(((.(((.(((((..(((...---..))).))))).))).)))..))..)...))).))).(((.....))))).)) ( -34.90)
>DroYak_CAF1 82391 98 + 1
AUCAUCAAUCCGCCGCGAGUGGCCACCAACGAAGCUGGCCAGUUAA---CCACUUCCAGCAUCGAUGGCAGCUGCCAGGCGAGGAUCUGAAGAUCU-GAGGA
........((((((..(.(..((..(((.(((.(((((..(((...---..))).))))).))).)))..))..)).)))..(((((....)))))-..))) ( -36.50)
>consensus
AUCAUCAAUCCGCUGCGAGUGGCCACCAACGAAGCUGGCCAGUUAACAACCACUUCCAGCGCCGAUGGCAGCUGCCAGGCGAGGAUCUGGGGAU________
(((.(((((((..(((..(..((..(((.((..(((((..(((........))).)))))..)).)))..))..)...))).)))).))).)))........ (-28.40 = -28.36 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	8,691,829 – 8,691,923
Length	94
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	87.37
Mean single sequence MFE	-39.28
Consensus MFE	-30.14
Energy contribution	-30.78
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.00
Structure conservation index	0.77
SVM decision value	0.85
SVM RNA-class probability	0.866330
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8691829 94 - 23771897
--------AUCCCCAGAUCCUCGCCUGGCAGCUGCCAUCGGCGCUGGAAGUGGUUGUUAACUGGCCAGCUUCGUUGGUGGCCACUCGCAGCGGAUUGAUGUU
--------.......(((((..(((((((....))))..)))((((..((((((..(((((.((....))..)))))..))))))..)))))))))...... ( -39.90)
>DroSec_CAF1 79679 94 - 1
--------AUCCCCAGAUCCUCGCCUGGCAGCUGCCAUCGGCGCUGGAAGUGGUUGUUAACCGGCCAGCUACGUUGGUGGCCACUCGCAGCGGAUUGAUGAU
--------(((....(((((..(((((((....))))..)))((((..((((((..(((((.((....))..)))))..))))))..)))))))))...))) ( -39.60)
>DroSim_CAF1 80185 94 - 1
--------AUCCCCAGAUCCUCGCCUGGCAGCUGACAUCGGCGCUGGAAGUGGUUGUUAACUGGCCAGCUUCGUUGGUGGCCACUCGCAGUGGAUUGAUGAU
--------(((....(((((.((((..((.((((....))))))..).((((((..(((((.((....))..)))))..)))))).)).).)))))...))) ( -34.20)
>DroEre_CAF1 84279 99 - 1
UCCUCCUGAUCCUCAGUUCCUCGCCUGGCAGCUGCCAUCGAUGCUGGAAGUGG---GUAACUGGCCAGCUUCGUUGGUGGCCACUUGCGGCGGAUUGAUGAU
........(((.(((((((.((((..((..((..(((.(((.(((((.(((..---...)))..))))).))).)))..))..)).)))).))))))).))) ( -42.50)
>DroYak_CAF1 82391 98 - 1
UCCUC-AGAUCUUCAGAUCCUCGCCUGGCAGCUGCCAUCGAUGCUGGAAGUGG---UUAACUGGCCAGCUUCGUUGGUGGCCACUCGCGGCGGAUUGAUGAU
.....-..(((.((((.(((((((..(...((..(((.(((.(((((.(((..---...)))..))))).))).)))..))..)..)))).))))))).))) ( -40.20)
>consensus
________AUCCCCAGAUCCUCGCCUGGCAGCUGCCAUCGGCGCUGGAAGUGGUUGUUAACUGGCCAGCUUCGUUGGUGGCCACUCGCAGCGGAUUGAUGAU
...............(((((.(((..((..(((((((.(((.(((((.(((........)))..))))).))).)))))))..)).)).).)))))...... (-30.14 = -30.78 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:54 2006