Locus 6032

Sequence ID 3R_DroMel_CAF1
Location 15,900,519 – 15,900,668
Length 149
Max. P 0.721235
window9839 window9840 window9841

overview

Window 9

Location 15,900,519 – 15,900,614
Length 95
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 91.04
Mean single sequence MFE -20.82
Consensus MFE -17.11
Energy contribution -17.07
Covariance contribution -0.04
Combinations/Pair 1.10
Mean z-score -1.29
Structure conservation index 0.82
SVM decision value -0.05
SVM RNA-class probability 0.506542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15900519 95 + 27905053
AACUUUCUGUUAUUGUUGCCACAAACUAUAACAAGGCGCUUAAAAUAUAUAAAAUAUUGUUUUCGUUUGUGGG---AUGGCAGCAAAUGCAUGGAUUG
....((((((..(((((((((....((((((....(((.....(((((.....))))).....))))))))).---.)))))))))..))).)))... ( -21.40)
>DroSec_CAF1 7804 98 + 1
AACUUUCUGUUAUUGUUGCCACAAACUAUAACAAGGCGCUUAAAAUAUAUAAAAUAUUGUUUCCGUUUGUGGGAGGAUGGCAGCGAAUGCAUGGAUUG
....((((((..((((((((((...((((((....(((.....(((((.....))))).....)))))))))...).)))))))))..))).)))... ( -22.30)
>DroSim_CAF1 7853 98 + 1
AACUUUCUGUUAUUGUUGCCACAAACUAUAACAAGGCGCUUAAAAUAUAUAAAAUAUUGUUUUCGUUUGUGGGAGGAUGACAGCGAAUGCAUGGAUUG
...((.((((((((.((.((((((((...(((((......................)))))...)))))))))).)))))))).))............ ( -22.65)
>DroEre_CAF1 7434 95 + 1
AACUUUCUGUUAUUGUUGCCACAAACUAUAACAAGGCGCUUAAAAUAUAUAAAAUAUUGUUUUCGUUUGUGGG---AUGCCAGCGAAUGCAUGGAUCG
..................((((((((...(((((......................)))))...))))))))(---((.(((((....)).)))))). ( -19.45)
>DroAna_CAF1 2089 87 + 1
AACUUUUUGUUAUUGUUGCCACAAACUAUAACAAGGCGCUUAAAA-AUAUAAAAUAUUGUUUUCGUUUGUGGG---AUUGCAAC----GCAAAGA---
...(((((((..(((((.((((((((...(((((.....(((...-...)))....)))))...)))))))).---)..)))).----)))))))--- ( -18.30)
>consensus
AACUUUCUGUUAUUGUUGCCACAAACUAUAACAAGGCGCUUAAAAUAUAUAAAAUAUUGUUUUCGUUUGUGGG___AUGGCAGCGAAUGCAUGGAUUG
......(((((((.....((((((((...(((((......................)))))...))))))))....)))))))............... (-17.11 = -17.07 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,900,578 – 15,900,668
Length 90
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 85.01
Mean single sequence MFE -27.30
Consensus MFE -15.80
Energy contribution -16.28
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -2.20
Structure conservation index 0.58
SVM decision value -0.05
SVM RNA-class probability 0.509249
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15900578 90 + 27905053
UUUUCGU-UUGUGGG---AUGGCAGCAAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGUAACAAACUCCCCGAACGAA---AAAAAGUCGA
(((((((-(((.(((---(..(((.....)))...................((((....)))).........))))))))))))---))........ ( -27.00)
>DroSec_CAF1 7863 96 + 1
UUUCCGU-UUGUGGGAGGAUGGCAGCGAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGGAACAAACUCCCCGAACGAAAGAAAAAAGUCGA
....(((-(((.(((((..(((((.....))).................(.((((....)))).)..))..)))))))))))............... ( -29.20)
>DroSim_CAF1 7912 96 + 1
UUUUCGU-UUGUGGGAGGAUGACAGCGAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGUAACAAACUCCCCGAACGAAAGAAAAAAGUCGA
(((((((-(((.(((((..(((((.(((...((.....))...)))...)))(((....))).....))..)))))))))))))))........... ( -31.00)
>DroEre_CAF1 7493 86 + 1
UUUUCGU-UUGUGGG---AUGCCAGCGAAUGCAUGGAUCGAAAUUGAAAUGUGCCUGAGGGCAA---CGAAUUCCCCGAACGACA----GAAACUGA
...((((-(((.(((---(((((..((...(((((..(((....)))..))))).))..)))).---.....)))))))))))((----(...))). ( -25.10)
>DroYak_CAF1 8740 90 + 1
UUUUCGUUUUGUGGG---AUGGCAGGGGAUGCAUGGUUUGAAAUUGAAAUGUGCCUGAGGGCAGCACCAAACUCCCCGAACGAAG----AAAGUCGA
(((((((((.(.(((---(.(.....((.(((...((((.......)))).((((....)))))))))...))))))))))))))----)....... ( -24.20)
>consensus
UUUUCGU_UUGUGGG___AUGGCAGCGAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGUAACAAACUCCCCGAACGAAA__AAAAAGUCGA
.((((((.(((.(((...(((.((.....))))).................((((....))))..........))))))))))))............ (-15.80 = -16.28 +   0.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,900,578 – 15,900,668
Length 90
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 85.01
Mean single sequence MFE -22.34
Consensus MFE -14.60
Energy contribution -14.76
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -2.14
Structure conservation index 0.65
SVM decision value 0.40
SVM RNA-class probability 0.721235
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15900578 90 - 27905053
UCGACUUUUU---UUCGUUCGGGGAGUUUGUUACUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUUGCUGCCAU---CCCACAA-ACGAAAA
........((---((((((.(((((..(((....((((....)))).....)))...........(((.....)))..)---))).).)-))))))) ( -21.20)
>DroSec_CAF1 7863 96 - 1
UCGACUUUUUUCUUUCGUUCGGGGAGUUUGUUCCUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUCGCUGCCAUCCUCCCACAA-ACGGAAA
............(((((((.((((((..((....((((....))))...................(((.....)))))..))))).).)-)))))). ( -24.90)
>DroSim_CAF1 7912 96 - 1
UCGACUUUUUUCUUUCGUUCGGGGAGUUUGUUACUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUCGCUGUCAUCCUCCCACAA-ACGAAAA
............(((((((.((((((..((....((((....))))................((.((....)))).))..))))).).)-)))))). ( -24.80)
>DroEre_CAF1 7493 86 - 1
UCAGUUUC----UGUCGUUCGGGGAAUUCG---UUGCCCUCAGGCACAUUUCAAUUUCGAUCCAUGCAUUCGCUGGCAU---CCCACAA-ACGAAAA
........----..(((((.(((((....(---(.(((....)))))..............(((.((....)))))..)---))).).)-))))... ( -19.90)
>DroYak_CAF1 8740 90 - 1
UCGACUUU----CUUCGUUCGGGGAGUUUGGUGCUGCCCUCAGGCACAUUUCAAUUUCAAACCAUGCAUCCCCUGCCAU---CCCACAAAACGAAAA
........----.((((((.(((((((.((((..((((....))))..............)))).)).)))))((....---....)).)))))).. ( -20.89)
>consensus
UCGACUUUUU__UUUCGUUCGGGGAGUUUGUUACUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUCGCUGCCAU___CCCACAA_ACGAAAA
.............(((((..((((((.(((....((((....)))).....))).))).......(((.....)))......))).....))))).. (-14.60 = -14.76 +   0.16)

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 12:10:54 2006