Locus 7424

Sequence ID 2L_DroMel_CAF1
Location 20,613,354 – 20,613,589
Length 235
Max. P 0.916475
window11932 window11933 window11934 window11935

overview

Window 2

Location 20,613,354 – 20,613,456
Length 102
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 64.99
Mean single sequence MFE -25.46
Consensus MFE -4.90
Energy contribution -6.23
Covariance contribution 1.33
Combinations/Pair 1.15
Mean z-score -2.95
Structure conservation index 0.19
SVM decision value 1.11
SVM RNA-class probability 0.916475
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20613354 102 + 22407834
AGUAGGCCAAAACAAAAAGCCUGCAAGGCAACAAAGACACGCACACAU----UGGUGCCUGUGAGGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCAGCCC
.((((((...........))))))..(((.......(((.((((....----..)))).)))..(((.((.((.(((((((.....))))))))))).))).))). ( -37.70)
>DroPse_CAF1 190028 83 + 1
CAGAAAAUAUACACAAAAGCCUGCAGGGCAACAAAGGG-UGCACACAU----C-------------CACAUCCACAUCCACUG-----GCACAUUUGCAUCCACAC
..................(((.....)))......(((-((((.....----(-------------((.............))-----)......))))))).... ( -15.52)
>DroSec_CAF1 132397 102 + 1
AGUAGGCCAAAACAAAAAGCCUGCCAGGCAACAAAGCCACGCACACAU----UGGUGCCUGUGACGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCCACCC
.((((((...........))))))..(((......)))..((((....----..))))..(((.((((...((.(((((((.....)))))))))))))..))).. ( -32.50)
>DroSim_CAF1 128407 102 + 1
AGUAGGCCAAAACAAAAAGCCUGCCAGGCAACAAAGGCACGCACACAU----CGGUGCCUGUGACGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCCACCC
.((.(((...........((.((((.(....)...)))).))...(((----(.((((.((.((((((((....)))))...))))).)))).)))).))).)).. ( -34.90)
>DroYak_CAF1 122057 89 + 1
AGAAUUCCAAAACAAAAAGCCUACCAGGCAACAAAGGCUCGCCCACACAGAGUAGUGUCUUCAACGCACACACAU--GCAUUGUCCACACA---------------
..................(((.....))).......((((.........)))).((((...(((.(((......)--)).)))...)))).--------------- ( -16.60)
>DroPer_CAF1 195706 83 + 1
CAGAAAAUAUACACAAAAGCCUGCAGGGCAACAAAGGG-UGCACACAU----C-------------CACAUCCACAUCCACUG-----GCACAUUUGCAUCCACAC
..................(((.....)))......(((-((((.....----(-------------((.............))-----)......))))))).... ( -15.52)
>consensus
AGUAGGCCAAAACAAAAAGCCUGCAAGGCAACAAAGGCACGCACACAU____CGGUGCCUGUGACGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCCACCC
..................(((.....)))..........((((...........((((.......))))............((......))....))))....... ( -4.90 =  -6.23 +   1.33)

alignment

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secondary structure

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Window 3

Location 20,613,456 – 20,613,574
Length 118
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 84.22
Mean single sequence MFE -24.77
Consensus MFE -19.68
Energy contribution -20.85
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.79
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20613456 118 + 22407834
A-CUCACACUCACACACACACGUGCAUACCACUCGGAGGAAUUGUCAUUAUACAAUGCAACCGUGAAUAAUAGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCC
.-.((((.....(((......)))..........((..(.(((((......))))).)..))))))......(((((.....((((.(((.((((.....)))).))).)))).))))) ( -29.30)
>DroSec_CAF1 132499 112 + 1
U-CUCUCACACACACACA---ACACACACUACUCGGAGAAAUUGUCAUCAUACAAUGCAACCGUGAAUAAAAGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCA---
.-................---..........(.(((....(((((......)))))....))).).......((.....)).((((.(((.((((.....)))).))).))))...--- ( -17.90)
>DroSim_CAF1 128509 115 + 1
U-CUCUCACACACACACA---ACACACACCACUCGGAGGAAUUGUCAUUAUACAAUGCAACCGUGAAUAAUAGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCC
.-...((((.........---.......((....)).((..(((.((((....)))))))))))))......(((((.....((((.(((.((((.....)))).))).)))).))))) ( -27.00)
>DroEre_CAF1 118143 99 + 1
----------------C----GCGCACACCACUCGGAGGAAUUGUCAUUAAACAAUGCACCCGUGAAUAAUGGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCC
----------------.----((((......(.(((..(.(((((......))))).)..))).).....((((....))))((((.(((.((((.....)))).))).)))))).)). ( -27.90)
>DroYak_CAF1 122146 113 + 1
--CUCUCACACGCUCGU----GAACACACCACUCGGAGGAAUUGUCAUUAUACAAUGCAACCGUGAAUAAUAGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCC
--...((((......((----(.......)))..((..(.(((((......))))).)..))))))......(((((.....((((.(((.((((.....)))).))).)))).))))) ( -29.40)
>DroAna_CAF1 126977 113 + 1
UACCCACCUACACACAUA---CCACA---CACUCGCACGAAUUGUCAUUAUACAAUGCAUCCGUAAAUAAUAGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAAGC
..................---.....---.....(((((...((.((((....))))))..)))..................((((.(((.((((.....)))).))).)))))).... ( -17.10)
>consensus
U_CUCUCACACACACACA___GCACACACCACUCGGAGGAAUUGUCAUUAUACAAUGCAACCGUGAAUAAUAGGCUGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCC
...............................(.(((....(((((......)))))....))).).......(((((.....((((.(((.((((.....)))).))).)))).))))) (-19.68 = -20.85 +   1.17)

alignment

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secondary structure

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Window 4

Location 20,613,495 – 20,613,589
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.47
Mean single sequence MFE -22.63
Consensus MFE -13.95
Energy contribution -14.12
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.28
Structure conservation index 0.62
SVM decision value 1.10
SVM RNA-class probability 0.914490
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20613495 94 + 22407834
AUUGUCAUUAUACAAUGCAACCGUGAAUAAUAGGC-UGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCCCAUAACAAUAACGCA-------------------------
.(((.((((....))))))).(((........(((-((.....((((.(((.((((.....)))).))).)))).)))))..........)))..------------------------- ( -21.47)
>DroPse_CAF1 190125 95 + 1
AUUGUCAUUAUACAAUGCAGCCGUGAAUAAUAGGCCCGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAAGCAAUAACAAUAACACA-------------------------
(((((.(((......(((.(((..........)))........((((.(((.((((.....)))).))).)))))))...))).)))))......------------------------- ( -18.80)
>DroSec_CAF1 132535 76 + 1
AUUGUCAUCAUACAAUGCAACCGUGAAUAAAAGGC-UGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCA-------------------------------------------
(((((......)))))((..............((.-....)).((((.(((.((((.....)))).))).)))))).------------------------------------------- ( -14.90)
>DroEre_CAF1 118163 94 + 1
AUUGUCAUUAAACAAUGCACCCGUGAAUAAUGGGC-UGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAGCCCAAUACAAUAUCGCA-------------------------
(((((......)))))......((((.((.(((((-((.....((((.(((.((((.....)))).))).)))).))))))).)).....)))).------------------------- ( -27.40)
>DroAna_CAF1 127011 119 + 1
AUUGUCAUUAUACAAUGCAUCCGUAAAUAAUAGGC-UGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAAGCCAUGACAAUAACGCCCCCCGCCUACUUGGGGAAAAACCAC
((((((((.......(((....))).......(((-(......((((.(((.((((.....)))).))).))))...))))))))))))......(((((......)))))......... ( -32.30)
>DroPer_CAF1 195803 95 + 1
AUUGUCAUUAUACAAUGGAGCCGUGAAUAAUAGGCCCGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAAGCAAUAACAAUAACACA-------------------------
(((((.(((......(((.(((..........)))))).....((((.(((.((((.....)))).))).))))......))).)))))......------------------------- ( -20.90)
>consensus
AUUGUCAUUAUACAAUGCAACCGUGAAUAAUAGGC_UGACCCAGAUGAGGUGCAUUAACCAAAUGAACCGCAUCGCAAGCCAUAACAAUAACGCA_________________________
(((((......)))))((..............((......)).((((.(((.((((.....)))).))).))))))............................................ (-13.95 = -14.12 +   0.17)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,613,495 – 20,613,589
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.47
Mean single sequence MFE -27.09
Consensus MFE -19.45
Energy contribution -21.40
Covariance contribution 1.95
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.72
SVM decision value 0.70
SVM RNA-class probability 0.827584
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20613495 94 - 22407834
-------------------------UGCGUUAUUGUUAUGGGCUGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCA-GCCUAUUAUUCACGGUUGCAUUGUAUAAUGACAAU
-------------------------...((((((((.(((((((((((((.(((.((((.....)))).))).))))...).))-)))))).....(((((...)))))))))))))... ( -26.50)
>DroPse_CAF1 190125 95 - 1
-------------------------UGUGUUAUUGUUAUUGCUUGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCGGGCCUAUUAUUCACGGCUGCAUUGUAUAAUGACAAU
-------------------------......((((((((((..((((((((((((....((..(((((..(((.((....)).)))..)))))..)).)))))))))))))))))))))) ( -28.00)
>DroSec_CAF1 132535 76 - 1
-------------------------------------------UGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCA-GCCUUUUAUUCACGGUUGCAUUGUAUGAUGACAAU
-------------------------------------------((((((((((..((...(((......))).....))..))(-(((..........)))))))))))).......... ( -17.40)
>DroEre_CAF1 118163 94 - 1
-------------------------UGCGAUAUUGUAUUGGGCUGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCA-GCCCAUUAUUCACGGGUGCAUUGUUUAAUGACAAU
-------------------------((((.....(((.((((((((((((.(((.((((.....)))).))).))))...).))-))))).))).......))))(((((....))))). ( -29.30)
>DroAna_CAF1 127011 119 - 1
GUGGUUUUUCCCCAAGUAGGCGGGGGGCGUUAUUGUCAUGGCUUGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCA-GCCUAUUAUUUACGGAUGCAUUGUAUAAUGACAAU
.......((((((........))))))....((((((((....(((((((((((.((((.....)))).))).....((((...-.))))............))))))))..)))))))) ( -35.30)
>DroPer_CAF1 195803 95 - 1
-------------------------UGUGUUAUUGUUAUUGCUUGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCGGGCCUAUUAUUCACGGCUCCAUUGUAUAAUGACAAU
-------------------------......((((((((((..(((((((.(((.((((.....)))).))).))))(((((((.............)))).)))..))))))))))))) ( -26.02)
>consensus
_________________________UGCGUUAUUGUUAUGGCUUGCGAUGCGGUUCAUUUGGUUAAUGCACCUCAUCUGGGUCA_GCCUAUUAUUCACGGCUGCAUUGUAUAAUGACAAU
...............................((((((((....(((((((((((.((((.....)))).))).....((((.....))))............))))))))..)))))))) (-19.45 = -21.40 +   1.95)

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 12:36:32 2006