Locus 4320

Sequence ID 3R_DroMel_CAF1
Location 11,441,347 – 11,441,484
Length 137
Max. P 0.996563
window7055 window7056 window7057 window7058

overview

Window 5

Location 11,441,347 – 11,441,444
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.14
Mean single sequence MFE -33.66
Consensus MFE -28.10
Energy contribution -28.14
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -2.75
Structure conservation index 0.83
SVM decision value 2.72
SVM RNA-class probability 0.996563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11441347 97 + 27905053
----UAAUUGUUAUG-------------------AUUUAAGCCCAUAUGCUUUGCCGAUGCAGGAGUAUCCCCCAAAAGGGAUAUCGAUAAAUGCAGGCAAAUAUUGCAAUGGCGAGGCC
----...........-------------------..............(((((((((.(((((((.((((((......))))))))......((....))....))))).))))))))). ( -28.10)
>DroSec_CAF1 181286 116 + 1
----UAAUUGUUAUGUUGAUUUAAAUAAACUAUUAUUUAAGCCGAUAUGCCUUGCCGAUGCAUGGGUAUCCCCCACAAGGGAUAUCGGUAAAUGCUGGCAAAUAUUGCAAUGGCGAGGCC
----........((((((..((((((((....))))))))..))))))(((((((((.((((..((((((((......))))))))(((....))).........)))).))))))))). ( -41.80)
>DroSim_CAF1 175495 116 + 1
----UAAUUGUUAUGUUGAUUUAAAUAAACUAUUAUUUAAGCCCAUAUGCCUUGCCGAUGCAUGGGUAUCCCCCACAAGGGAUAUCGGUAAAUGCUGGCAAAUAUUGCAAUGGCGAGGCC
----........((((.(..((((((((....))))))))..).))))(((((((((.((((..((((((((......))))))))(((....))).........)))).))))))))). ( -38.00)
>DroEre_CAF1 170787 111 + 1
GUUAUAACUAUUAUC-CCACUUAAACAAACU--GGU-UCAGCCCAUAUGCUUUGCCGAUGCAGGAGUAUCCC-----AGGGAUAUUGGUAAAUGCAGGCAAAUAUUGCAAUGGCGAGGCC
((....((((.((((-((.............--(((-..(((......)))..)))(((((....)))))..-----.)))))).))))....)).(((.....((((....)))).))) ( -30.80)
>DroYak_CAF1 174201 119 + 1
ACCAUAACUAUUAUUUUCAUUUAAGUAAACUAUGAU-UCAACCCAUAUGCUUGGCCGAUGCAGUAGUAUGCCCCAGAAGGGAUAUUGGUAAAUGCACGCAAAUAUUGCAAUGGCGAGGCC
..((((....((((((......))))))..))))..-...........((((.((((.(((((((...((((((....))).((((....))))...)))..))))))).)))).)))). ( -29.60)
>consensus
____UAAUUGUUAUGUUCAUUUAAAUAAACUAUGAUUUAAGCCCAUAUGCUUUGCCGAUGCAGGAGUAUCCCCCACAAGGGAUAUCGGUAAAUGCAGGCAAAUAUUGCAAUGGCGAGGCC
................................................(((((((((.((((..((((((((......))))))))......((....)).....)))).))))))))). (-28.10 = -28.14 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,441,347 – 11,441,444
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.14
Mean single sequence MFE -27.52
Consensus MFE -19.48
Energy contribution -20.28
Covariance contribution 0.80
Combinations/Pair 1.09
Mean z-score -1.42
Structure conservation index 0.71
SVM decision value -0.01
SVM RNA-class probability 0.528536
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11441347 97 - 27905053
GGCCUCGCCAUUGCAAUAUUUGCCUGCAUUUAUCGAUAUCCCUUUUGGGGGAUACUCCUGCAUCGGCAAAGCAUAUGGGCUUAAAU-------------------CAUAACAAUUA----
......(((..(((....((((((((((......(((((((((....))))))).)).))))..)))))))))....)))......-------------------...........---- ( -25.40)
>DroSec_CAF1 181286 116 - 1
GGCCUCGCCAUUGCAAUAUUUGCCAGCAUUUACCGAUAUCCCUUGUGGGGGAUACCCAUGCAUCGGCAAGGCAUAUCGGCUUAAAUAAUAGUUUAUUUAAAUCAACAUAACAAUUA----
.((((.(((..((((.((..((....))..))....(((((((....)))))))....))))..))).)))).....(..((((((((....))))))))..).............---- ( -32.70)
>DroSim_CAF1 175495 116 - 1
GGCCUCGCCAUUGCAAUAUUUGCCAGCAUUUACCGAUAUCCCUUGUGGGGGAUACCCAUGCAUCGGCAAGGCAUAUGGGCUUAAAUAAUAGUUUAUUUAAAUCAACAUAACAAUUA----
.((((.(((..((((.((..((....))..))....(((((((....)))))))....))))..))).)))).(((((..((((((((....))))))))..)..)))).......---- ( -33.00)
>DroEre_CAF1 170787 111 - 1
GGCCUCGCCAUUGCAAUAUUUGCCUGCAUUUACCAAUAUCCCU-----GGGAUACUCCUGCAUCGGCAAAGCAUAUGGGCUGA-ACC--AGUUUGUUUAAGUGG-GAUAAUAGUUAUAAC
(((...)))..((((.........))))........((((((.-----(((.....)))((....)).(((((..(((.....-.))--)...)))))....))-))))........... ( -23.20)
>DroYak_CAF1 174201 119 - 1
GGCCUCGCCAUUGCAAUAUUUGCGUGCAUUUACCAAUAUCCCUUCUGGGGCAUACUACUGCAUCGGCCAAGCAUAUGGGUUGA-AUCAUAGUUUACUUAAAUGAAAAUAAUAGUUAUGGU
((((........(((.....)))(((((.......((..(((....)))..)).....))))).))))((((.(((((.....-.))))))))).......................... ( -23.30)
>consensus
GGCCUCGCCAUUGCAAUAUUUGCCUGCAUUUACCGAUAUCCCUUGUGGGGGAUACUCCUGCAUCGGCAAAGCAUAUGGGCUUAAAUAAUAGUUUAUUUAAAUCAACAUAACAAUUA____
......(((..(((....((((((((((........(((((((....)))))))....))))..)))))))))....)))........................................ (-19.48 = -20.28 +   0.80)

alignment

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secondary structure

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Window 7

Location 11,441,364 – 11,441,484
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.96
Mean single sequence MFE -41.92
Consensus MFE -36.32
Energy contribution -36.80
Covariance contribution 0.48
Combinations/Pair 1.03
Mean z-score -1.95
Structure conservation index 0.87
SVM decision value 1.61
SVM RNA-class probability 0.967395
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11441364 120 + 27905053
GCCCAUAUGCUUUGCCGAUGCAGGAGUAUCCCCCAAAAGGGAUAUCGAUAAAUGCAGGCAAAUAUUGCAAUGGCGAGGCCAUUGUCAUGGCGACGGUCGCAUAUAAGGAGGCGGCUGGCU
(((.......((((((..((((...(((((((......))))))).......))))))))))....((((((((...))))))))...)))..(((((((..........)))))))... ( -42.80)
>DroSec_CAF1 181322 111 + 1
GCCGAUAUGCCUUGCCGAUGCAUGGGUAUCCCCCACAAGGGAUAUCGGUAAAUGCUGGCAAAUAUUGCAAUGGCGAGGCCAUUGUCAUGGCGACGGUCGCAUAUAAGGAGG---------
.((((((.(((((((((.((((..((((((((......))))))))(((....))).........)))).)))))))))...))))...(((.....)))......))...--------- ( -42.80)
>DroSim_CAF1 175531 120 + 1
GCCCAUAUGCCUUGCCGAUGCAUGGGUAUCCCCCACAAGGGAUAUCGGUAAAUGCUGGCAAAUAUUGCAAUGGCGAGGCCAUUGUCAUGGCGACGGUCGCAUAUAAGGAGGCGGCUGGCU
(((((...(((((((((.((((..((((((((......))))))))(((....))).........)))).)))))))))...))....)))..(((((((..........)))))))... ( -47.70)
>DroEre_CAF1 170823 111 + 1
GCCCAUAUGCUUUGCCGAUGCAGGAGUAUCCC-----AGGGAUAUUGGUAAAUGCAGGCAAAUAUUGCAAUGGCGAGGCCAUUGUCAUGGCGACGGUCGCAUAUAAGGAGCA----GGCC
((((((((((.((((((.(((((.(((((((.-----..)))))))......((....))....))))).))))))((((.((((....)))).))))))))))..)).)).----.... ( -38.20)
>DroYak_CAF1 174240 116 + 1
ACCCAUAUGCUUGGCCGAUGCAGUAGUAUGCCCCAGAAGGGAUAUUGGUAAAUGCACGCAAAUAUUGCAAUGGCGAGGCCAUUGUCAUGGCGACGGUCGCCUAUAAGGAGGA----GGCC
........((((.((((.(((((((...((((((....))).((((....))))...)))..))))))).)))).))))....(((.....)))((((.(((......))).----)))) ( -38.10)
>consensus
GCCCAUAUGCUUUGCCGAUGCAGGAGUAUCCCCCACAAGGGAUAUCGGUAAAUGCAGGCAAAUAUUGCAAUGGCGAGGCCAUUGUCAUGGCGACGGUCGCAUAUAAGGAGGA____GGCC
.((.((((((.((((((.((((..((((((((......))))))))......((....)).....)))).))))))((((.((((....)))).))))))))))..))............ (-36.32 = -36.80 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,441,364 – 11,441,484
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.96
Mean single sequence MFE -35.94
Consensus MFE -34.36
Energy contribution -35.16
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.96
SVM decision value 1.41
SVM RNA-class probability 0.951175
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11441364 120 - 27905053
AGCCAGCCGCCUCCUUAUAUGCGACCGUCGCCAUGACAAUGGCCUCGCCAUUGCAAUAUUUGCCUGCAUUUAUCGAUAUCCCUUUUGGGGGAUACUCCUGCAUCGGCAAAGCAUAUGGGC
........((((....((((((....(..(((((....)))))..)(((..(((((((..((....))..))).(((((((((....))))))).)).))))..)))...)))))))))) ( -39.30)
>DroSec_CAF1 181322 111 - 1
---------CCUCCUUAUAUGCGACCGUCGCCAUGACAAUGGCCUCGCCAUUGCAAUAUUUGCCAGCAUUUACCGAUAUCCCUUGUGGGGGAUACCCAUGCAUCGGCAAGGCAUAUCGGC
---------......((.((((...((..(((((....)))))..)).....(((.....)))..)))).))(((((((.(((((((((.....)))))((....)))))).))))))). ( -35.60)
>DroSim_CAF1 175531 120 - 1
AGCCAGCCGCCUCCUUAUAUGCGACCGUCGCCAUGACAAUGGCCUCGCCAUUGCAAUAUUUGCCAGCAUUUACCGAUAUCCCUUGUGGGGGAUACCCAUGCAUCGGCAAGGCAUAUGGGC
..(((...(((........(((((.((..(((((....)))))..))...)))))....(((((.((((.....(.(((((((....))))))).).))))...))))))))...))).. ( -39.20)
>DroEre_CAF1 170823 111 - 1
GGCC----UGCUCCUUAUAUGCGACCGUCGCCAUGACAAUGGCCUCGCCAUUGCAAUAUUUGCCUGCAUUUACCAAUAUCCCU-----GGGAUACUCCUGCAUCGGCAAAGCAUAUGGGC
....----.....(((((((((...........((.(((((((...)))))))))...((((((((((........(((((..-----.)))))....))))..))))))))))))))). ( -31.90)
>DroYak_CAF1 174240 116 - 1
GGCC----UCCUCCUUAUAGGCGACCGUCGCCAUGACAAUGGCCUCGCCAUUGCAAUAUUUGCGUGCAUUUACCAAUAUCCCUUCUGGGGCAUACUACUGCAUCGGCCAAGCAUAUGGGU
((((----...........((((.....)))).((.(((((((...)))))))))........(((((.......((..(((....)))..)).....))))).))))............ ( -33.70)
>consensus
AGCC____GCCUCCUUAUAUGCGACCGUCGCCAUGACAAUGGCCUCGCCAUUGCAAUAUUUGCCUGCAUUUACCGAUAUCCCUUGUGGGGGAUACUCCUGCAUCGGCAAAGCAUAUGGGC
.............(((((((((....(..(((((....)))))..)(((..((((.((..((....))..))....(((((((....)))))))....))))..)))...))))))))). (-34.36 = -35.16 +   0.80)

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 11:26:05 2006