Locus 1494

Sequence ID 2R_DroMel_CAF1
Location 5,665,963 – 5,666,103
Length 140
Max. P 0.938567
window2533 window2534 window2535

overview

Window 3

Location 5,665,963 – 5,666,082
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.86
Mean single sequence MFE -35.52
Consensus MFE -25.38
Energy contribution -24.94
Covariance contribution -0.44
Combinations/Pair 1.29
Mean z-score -1.61
Structure conservation index 0.71
SVM decision value 0.46
SVM RNA-class probability 0.746746
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5665963 119 - 20766785
UUUC-CUAAAGAUUCCUGAUGGUGUUCACCUGCCUGGCGCUCAGUGUGUUUUCCACCAUCAAGGAGUACGAAGAGGACGCCGUCUACAUUCUGUUCCGCAUGGAGAUCCUGGUGGUUAUC
..((-((...((((((((((((((..((((((.........))).))).....))))))).)))))).)....))))((((((((.(((.(......).))).))))...))))...... ( -34.00)
>DroPse_CAF1 3224 118 - 1
--UCUUUCCAGAUUCCUGAUGGUGUUCACAUGCCUCGCCCUGAGCGUGUUUUCCACCAUCAAGGAGUACGAGGACGACGCCGUGUACAUUCUCUUUCGGAUGGAGAUCCUGGUUGUCAUC
--.....((((..(((((((((((...((((((.((.....))))))))....))))))).))))(((((.((......)).)))))..(((((.......)))))..))))........ ( -39.00)
>DroWil_CAF1 3206 119 - 1
GUUU-UUACAGAUUUCUGAUGGUGUUUACAUGUCUCGCAUUGAGCGUGUUUUCAACCAUCAGGGAAUACGAAGAAGAUGCUGUGUAUAUAUUAUUUAGAAUGGAAAUUUUAGUUGUUAUA
....-.(((((.(..((((((((....(((((.(((.....)))))))).....))))))))..)...(......)...)))))..((((....(((((((....)))))))....)))) ( -30.70)
>DroMoj_CAF1 3682 119 - 1
CUC-UUUAUAGAUUUCUGAUGGUGUUUACAUGUCUCGCAUUGAGCGUGUUUUCCACCAUCAAGGAAUAUGAGGAGGAUGCUGUAUAUAUAUUAUUUCGCAUGGAGAUCAUAGUUGUCAUC
(((-((((((..((..((((((((...(((((.(((.....))))))))....))))))))..)).)))))))))((((....(((..(((.(((((.....))))).)))..))))))) ( -35.30)
>DroAna_CAF1 3423 120 - 1
AUAUAUCUCAGAUUCCUGAUGGUGUUCACCUGCCUGGCUCUGAGCGUAUUCUCCACCAUCAAGGAGUACGAGGAGGACGCCGUCUACAUCCUGUUCCGAAUGGAGAUCCUGGUUGUCAUC
.....((((..(((((((((((((....((.....))....(((......)))))))))).))))))..))))..(((((((......(((..........))).....))).))))... ( -32.80)
>DroPer_CAF1 3055 118 - 1
--UCCUUUCAGAUUCCUGAUGGUGUUCACAUGCCUCGCCCUGAGCGUGUUUUCCACCAUCAAGGAGUACGAGGACGACGCCGUGUACAUUCUCUUUCGGAUGGAGAUCCUGGUUGUCAUC
--(((((....(((((((((((((...((((((.((.....))))))))....))))))).))))))..))))).(((((((.(.....(((((.......))))).).))).))))... ( -41.30)
>consensus
_UUC_UUACAGAUUCCUGAUGGUGUUCACAUGCCUCGCACUGAGCGUGUUUUCCACCAUCAAGGAGUACGAGGAGGACGCCGUGUACAUUCUAUUUCGAAUGGAGAUCCUGGUUGUCAUC
...........(((((((((((((...(((((.(((.....))))))))....))))))).))))))((.((((.....((((................))))...)))).))....... (-25.38 = -24.94 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,666,003 – 5,666,103
Length 100
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 77.48
Mean single sequence MFE -24.82
Consensus MFE -20.07
Energy contribution -19.35
Covariance contribution -0.72
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.81
SVM decision value 1.22
SVM RNA-class probability 0.932476
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5666003 100 + 20766785
GCGUCCUCUUCGUACUCCUUGAUGGUGGAAAACACACUGAGCGCCAGGCAGGUGAACACCAUCAGGAAUCUUUAG-GAAAUGAGCAAUCACAAAUUAUUGU---
((.((((........((((.(((((((.....(((.(((..(....).))))))..)))))))))))......))-)).....))................--- ( -25.64)
>DroVir_CAF1 3720 96 + 1
GCAUCCUCCUCGUAUUCUUUGAUGGUGGAAAACACGCUCAAUGCGAGACAUGUGAACACCAUCAGAAAACUGCAAA-AA----ACAAUACAAAAAUAUUAC---
...........(((((.((((((((((....(((.((((.....))).).)))...)))))))))).)).)))...-..----..................--- ( -21.20)
>DroPse_CAF1 3264 90 + 1
GCGUCGUCCUCGUACUCCUUGAUGGUGGAAAACACGCUCAGGGCGAGGCAUGUGAACACCAUCAGGAAUCUGGAAAGA----CAAGGUUACUAC----------
..(((.(((......((((.(((((((....(((.(((........))).)))...)))))))))))....)))..))----)...........---------- ( -27.70)
>DroSec_CAF1 3404 100 + 1
GCGUCCUCUUCGUACUCCUUGAUGGUGGAAAACACACUGAGCGCCAGGCAGGUGAACACCAUCAGGAAUCUUUAG-AAAAUUAAAAAUUACAAUUCAUUGU---
......(((......((((.(((((((.....(((.(((..(....).))))))..)))))))))))......))-)........................--- ( -22.00)
>DroSim_CAF1 3420 99 + 1
GCGUCCUCUUCGUACUCCUUGAUGGUGGAAAACACACUGAGCGCCAGGCAGGUGAACACCAUCAGGAAUCUUUAG-ACAAAAAGAAAUCGAAAAUUAUUG----
........((((...((((.(((((((.....(((.(((..(....).))))))..))))))))))).(((((..-....)))))...))))........---- ( -25.10)
>DroYak_CAF1 3265 104 + 1
GCGUCCUCUUCGUACUCCUUGAUGGUGGAAAACACACUGAGCGCCAGGCAGGUGAACACCAUCAGGAAUCUAAAAAAAAAUGAGAAAUCAAAAGAUUUCGUGAA
(((...((((.....((((.(((((((.....(((.(((..(....).))))))..))))))))))).............(((....))).))))...)))... ( -27.30)
>consensus
GCGUCCUCUUCGUACUCCUUGAUGGUGGAAAACACACUGAGCGCCAGGCAGGUGAACACCAUCAGGAAUCUUUAA_AAAAU_AAAAAUCAAAAAUUAUUGU___
.................((((((((((.....(((.(((.....)))....)))..))))))))))...................................... (-20.07 = -19.35 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,666,003 – 5,666,103
Length 100
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 77.48
Mean single sequence MFE -28.33
Consensus MFE -18.70
Energy contribution -18.32
Covariance contribution -0.39
Combinations/Pair 1.16
Mean z-score -1.95
Structure conservation index 0.66
SVM decision value 1.29
SVM RNA-class probability 0.938567
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5666003 100 - 20766785
---ACAAUAAUUUGUGAUUGCUCAUUUC-CUAAAGAUUCCUGAUGGUGUUCACCUGCCUGGCGCUCAGUGUGUUUUCCACCAUCAAGGAGUACGAAGAGGACGC
---((((....))))...........((-((...((((((((((((((..((((((.........))).))).....))))))).)))))).)....))))... ( -26.70)
>DroVir_CAF1 3720 96 - 1
---GUAAUAUUUUUGUAUUGU----UU-UUUGCAGUUUUCUGAUGGUGUUCACAUGUCUCGCAUUGAGCGUGUUUUCCACCAUCAAAGAAUACGAGGAGGAUGC
---...........(((((.(----((-((....(((((.((((((((...(((((.(((.....))))))))....)))))))).)))))..))))).))))) ( -26.70)
>DroPse_CAF1 3264 90 - 1
----------GUAGUAACCUUG----UCUUUCCAGAUUCCUGAUGGUGUUCACAUGCCUCGCCCUGAGCGUGUUUUCCACCAUCAAGGAGUACGAGGACGACGC
----------.........(((----(((((....(((((((((((((...((((((.((.....))))))))....))))))).))))))..))))))))... ( -32.70)
>DroSec_CAF1 3404 100 - 1
---ACAAUGAAUUGUAAUUUUUAAUUUU-CUAAAGAUUCCUGAUGGUGUUCACCUGCCUGGCGCUCAGUGUGUUUUCCACCAUCAAGGAGUACGAAGAGGACGC
---((((....)))).........((((-((....(((((((((((((..((((((.........))).))).....))))))).))))))....))))))... ( -25.10)
>DroSim_CAF1 3420 99 - 1
----CAAUAAUUUUCGAUUUCUUUUUGU-CUAAAGAUUCCUGAUGGUGUUCACCUGCCUGGCGCUCAGUGUGUUUUCCACCAUCAAGGAGUACGAAGAGGACGC
----..............((((((((((-......(((((((((((((..((((((.........))).))).....))))))).))))))))))))))))... ( -27.80)
>DroYak_CAF1 3265 104 - 1
UUCACGAAAUCUUUUGAUUUCUCAUUUUUUUUUAGAUUCCUGAUGGUGUUCACCUGCCUGGCGCUCAGUGUGUUUUCCACCAUCAAGGAGUACGAAGAGGACGC
.....((((((....))))))....((((((((..(((((((((((((..((((((.........))).))).....))))))).))))))..))))))))... ( -31.00)
>consensus
___ACAAUAAUUUGUGAUUUCU_AUUUU_CUAAAGAUUCCUGAUGGUGUUCACCUGCCUGGCGCUCAGUGUGUUUUCCACCAUCAAGGAGUACGAAGAGGACGC
...................................(((((((((((((..(((....(((.....))).))).....))))))).))))))............. (-18.70 = -18.32 +  -0.39)

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 10:06:10 2006