Locus 4225

Sequence ID 2L_DroMel_CAF1
Location 12,091,900 – 12,092,032
Length 132
Max. P 0.863800
window6670 window6671 window6672

overview

Window 0

Location 12,091,900 – 12,092,001
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.04
Mean single sequence MFE -28.70
Consensus MFE -14.62
Energy contribution -14.60
Covariance contribution -0.02
Combinations/Pair 1.29
Mean z-score -2.52
Structure conservation index 0.51
SVM decision value 0.69
SVM RNA-class probability 0.824429
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12091900 101 + 22407834
AAAUCGAGCA----------UCUUUCGCUGGAAGGAUGCGGAAAUGUUGAAAAAAAUA---------GCGAUGCGAUCAGCGAGCGUGAAAUCGCAGUCAGCAUAUGAAAAGGAUGUACA
..(((..(((----------((((((....)))))))))....(((((((........---------((..(((.....))).))(((....)))..)))))))........)))..... ( -28.50)
>DroSec_CAF1 28301 101 + 1
AAAUCGGGCA----------UCUUUCGCUGGAAGGAUGCCGAAAUGUUGGAAAAAAUA---------GCGCUGCGAUCAGCGAGCGUGAAAUCGCAACCAGCAUAUGAAAAGGAUAUACA
..(((.((((----------((((((....))))))))))...(((((((........---------.(((((....))))).(((......)))..)))))))........)))..... ( -36.30)
>DroEre_CAF1 28574 99 + 1
AAAUCGGGCA----------UCUUUCGCUGGAAGGAUACGGAAAUGUGGAAAA--AAA---------GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCCAGCAUAUGAAAAGGAUAUACA
...(((.(((----------((((((....)))))))..((...(((((....--...---------(((((((.....)).)))))....))))).)).))...)))............ ( -25.80)
>DroYak_CAF1 30421 101 + 1
AAAUCGGGCA----------UCUUUCGCUGGAAGGAUACGGAAAUGUCGGAAAAAAUA---------GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCUAGCAUAUGAAAAGGAUGUACA
.....(..((----------(((((.((((........(((.....))).......))---------))((((((((..((....))...))))))))...........)))))))..). ( -28.26)
>DroAna_CAF1 29833 102 + 1
AAAUCGCGCC----------UCCUUCCCAGUAAGGAUGCUGAAAA-UUGAAAAAAAUAA-------AACACCGCGAUCAGCGACCGUGAAAUCGCAGCCAAUAUAUGGAUAGGAUAUGCA
.....(((..----------((((..(((....((.((((((...-.............-------..........)))))).))(((....)))..........)))..))))..))). ( -23.47)
>DroPer_CAF1 32399 118 + 1
AAAUUGCGCCUCUUCCACCUUCUUUCGCUGGAAGGAUGCGGAAAAGUCGGAAAAAAUAAAUAUAUAAAUGCUGCGAUCAGUGACCGUGAAAUCGCAGCCAAUAUAUGGAAAGGUUAUA--
.......((((.((((.((((((......))))))........................((((((....((((((((((.......)))..)))))))..))))))))))))))....-- ( -29.90)
>consensus
AAAUCGGGCA__________UCUUUCGCUGGAAGGAUGCGGAAAUGUUGAAAAAAAUA_________GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCCAGCAUAUGAAAAGGAUAUACA
..(((...............((((((....))))))...............................((((((((((..((....))...))))))))..))..........)))..... (-14.62 = -14.60 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,091,930 – 12,092,032
Length 102
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.11
Mean single sequence MFE -25.83
Consensus MFE -14.34
Energy contribution -16.45
Covariance contribution 2.11
Combinations/Pair 1.23
Mean z-score -2.24
Structure conservation index 0.55
SVM decision value 0.84
SVM RNA-class probability 0.863800
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12091930 102 + 22407834
GAAAUGUUGAAAAAAAUA--GCGAUGCGAUCAGCGAGCGUGAAAUCGCAGUCAGCAUAUGAAAAGGAUGUACAGGAUCGUAUCCUGGCAAAGUUCCUGCAAA-AA--------
...(((((((........--((..(((.....))).))(((....)))..))))))).((...(((((((.((((((...)))))))))....)))).))..-..-------- ( -26.30)
>DroSec_CAF1 28331 102 + 1
GAAAUGUUGGAAAAAAUA--GCGCUGCGAUCAGCGAGCGUGAAAUCGCAACCAGCAUAUGAAAAGGAUAUACAGGAUCGUAUCCUGGCAAAGUUCCUGCAAA-AA--------
...(((((((........--.(((((....))))).(((......)))..))))))).((...((((....((((((...)))))).......)))).))..-..-------- ( -30.30)
>DroSim_CAF1 28707 102 + 1
GAAAUGUUGGAAAAAAUA--GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCCAGCAUAUGAAAAGGAUAUACAGGAUCGUAUCCUGGCAAAGUUCCUGCAAA-AA--------
....(((.((((......--((((((((((..((....))...))))))))..))...((...(((((((........)))))))..))...)))).)))..-..-------- ( -30.50)
>DroEre_CAF1 28604 103 + 1
GAAAUGUGGAAAA--AAA--GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCCAGCAUAUGAAAAGGAUAUACAGGC---GAUCCUGGCAAAGUUCCCGAAAA-AAUGUG--UG
.............--...--(.((((((((..((....))...))))))))).((((((.....(((....((((.---...)))).......)))......-.)))))--). ( -25.00)
>DroYak_CAF1 30451 107 + 1
GAAAUGUCGGAAAAAAUA--GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCUAGCAUAUGAAAAGGAUGUACAUAA---GAUCCUGGCAAAGUUCCCGAAAA-AAUGUGUGUG
......((((........--((((((((((..((....))...))))))))..))...((...(((((.(.....)---.)))))..))......))))...-.......... ( -27.20)
>DroAna_CAF1 29863 96 + 1
GAAAA-UUGAAAAAAAUAAAACACCGCGAUCAGCGACCGUGAAAUCGCAGCCAAUAUAUGGAUAGGAUAUGCACAA--------------UAUUCCCAAAAAAAAUGUG--UG
.....-..............((((.(((((..((....))...)))))..........(((...((((((.....)--------------))))))))........)))--). ( -15.70)
>consensus
GAAAUGUUGAAAAAAAUA__GCGCUGCGAUCAGCGAGCGUGAAAUCGCAGCCAGCAUAUGAAAAGGAUAUACAGGA___UAUCCUGGCAAAGUUCCCGAAAA_AA________
...(((((((..........(((((((.....))).))))..........))))))).......(((....(((((.....))))).......)))................. (-14.34 = -16.45 +   2.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,091,930 – 12,092,032
Length 102
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.11
Mean single sequence MFE -22.00
Consensus MFE -15.62
Energy contribution -16.40
Covariance contribution 0.78
Combinations/Pair 1.28
Mean z-score -1.48
Structure conservation index 0.71
SVM decision value 0.60
SVM RNA-class probability 0.795627
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12091930 102 - 22407834
--------UU-UUUGCAGGAACUUUGCCAGGAUACGAUCCUGUACAUCCUUUUCAUAUGCUGACUGCGAUUUCACGCUCGCUGAUCGCAUCGC--UAUUUUUUUCAACAUUUC
--------..-...((((((....(((.(((((...))))))))..))))......((((.(((.((((........)))).).)))))).))--.................. ( -18.10)
>DroSec_CAF1 28331 102 - 1
--------UU-UUUGCAGGAACUUUGCCAGGAUACGAUCCUGUAUAUCCUUUUCAUAUGCUGGUUGCGAUUUCACGCUCGCUGAUCGCAGCGC--UAUUUUUUCCAACAUUUC
--------..-......((((....((((((((...))))))....................(((((((((...........)))))))))))--......))))........ ( -22.30)
>DroSim_CAF1 28707 102 - 1
--------UU-UUUGCAGGAACUUUGCCAGGAUACGAUCCUGUAUAUCCUUUUCAUAUGCUGGCUGCGAUUUCACGCUCGCUGAUCGCAGCGC--UAUUUUUUCCAACAUUUC
--------..-......((((....((((((((...))))))....................(((((((((...........)))))))))))--......))))........ ( -24.70)
>DroEre_CAF1 28604 103 - 1
CA--CACAUU-UUUUCGGGAACUUUGCCAGGAUC---GCCUGUAUAUCCUUUUCAUAUGCUGGCUGCGAUUUCACGCUCGCUGAUCGCAGCGC--UUU--UUUUCCACAUUUC
..--......-.....(((((....((((((...---.))))....................(((((((((...........)))))))))))--...--.)))))....... ( -24.80)
>DroYak_CAF1 30451 107 - 1
CACACACAUU-UUUUCGGGAACUUUGCCAGGAUC---UUAUGUACAUCCUUUUCAUAUGCUAGCUGCGAUUUCACGCUCGCUGAUCGCAGCGC--UAUUUUUUCCGACAUUUC
..........-...(((((((....((.(((((.---........)))))............(((((((((...........)))))))))))--.....)))))))...... ( -25.80)
>DroAna_CAF1 29863 96 - 1
CA--CACAUUUUUUUUGGGAAUA--------------UUGUGCAUAUCCUAUCCAUAUAUUGGCUGCGAUUUCACGGUCGCUGAUCGCGGUGUUUUAUUUUUUUCAA-UUUUC
..--.............((((((--------------(((((...(((....(((.....)))..(((((......))))).))))))))))))))...........-..... ( -16.30)
>consensus
________UU_UUUGCAGGAACUUUGCCAGGAUA___UCCUGUAUAUCCUUUUCAUAUGCUGGCUGCGAUUUCACGCUCGCUGAUCGCAGCGC__UAUUUUUUCCAACAUUUC
.................((((......(((((.....)))))....................(((((((((...........)))))))))..........))))........ (-15.62 = -16.40 +   0.78)

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 11:12:48 2006