Locus 8406

Sequence ID 3L_DroMel_CAF1
Location 22,099,466 – 22,099,669
Length 203
Max. P 0.999756
window13746 window13747 window13748 window13749 window13750 window13751 window13752 window13753

overview

Window 6

Location 22,099,466 – 22,099,574
Length 108
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 82.89
Mean single sequence MFE -36.82
Consensus MFE -25.05
Energy contribution -26.38
Covariance contribution 1.34
Combinations/Pair 1.17
Mean z-score -2.70
Structure conservation index 0.68
SVM decision value 0.64
SVM RNA-class probability 0.809996
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099466 108 + 23771897
AACGCCAGCGCCACC------GCCACCGC--CGCAAUAAUCCUGCAGCUCAGUCGAAAUGUCGCUGGCAAUCUAAGGAAAAGGAAAAAUGCCAGCGACAGCGGUGGGGAGUGGGUA
.......((.(((((------.(((((((--.(((.......))).............(((((((((((.(((........)))....)))))))))))))))))).).)))))). ( -47.30)
>DroSec_CAF1 85479 102 + 1
AACGCCAGCACCACC------GCCACCGC--CGCAAUAAUCCUGCAGCUCAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG------
.............((------.(((((((--.(((.......))).............(((((((((((.(((........)))....))))))))))))))))))))..------ ( -40.40)
>DroSim_CAF1 91957 102 + 1
AACGCCAGCACCACC------GCCACCGC--CGCAAUAAUCCUGCAGCUCAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG------
.............((------.(((((((--.(((.......))).............(((((((((((.(((........)))....))))))))))))))))))))..------ ( -40.40)
>DroEre_CAF1 84735 99 + 1
---GCUACCGCCACC------GCCACCGC--CGCAAUAAUCCUGCAGCUCAGUCGAAAUGUCUCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAACGACAGCGGUGAGGAG------
---....((..((((------((....((--.(((.......))).))..........((((..(((((.(((........)))....)))))..)))))))))).))..------ ( -29.70)
>DroYak_CAF1 103362 93 + 1
---GC------CACC------GCUAGCAC--CGCAAUAAUCCUGCAGCUGAGUCGAAAUGUCUCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG------
---.(------((((------((((((..--.(((.......))).))))........((((.((((((.(((........)))....)))))).)))))))))))....------ ( -34.30)
>DroPer_CAF1 104703 113 + 1
CGUGCCUGUGCCACACACUCAGCCA-UGCCGCACAAUAAUCCUGCAACUCAGUCGAAAUGUCGCUGGCAAUCUAAGAAAGAAGAAAAAUGCCAGCAACAUUGGUAGUGAAGGAG--
.((((..(((.....)))...((..-.)).)))).....((((...((((......(((((.(((((((.(((........)))....))))))).))))).).)))..)))).-- ( -28.80)
>consensus
AACGCCAGCGCCACC______GCCACCGC__CGCAAUAAUCCUGCAGCUCAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG______
......................(((((((...(((.......))).............(((((((((((.(((........)))....)))))))))))))))))).......... (-25.05 = -26.38 +   1.34) 

alignment

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secondary structure

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dotplot

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Window 7

Location 22,099,466 – 22,099,574
Length 108
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 82.89
Mean single sequence MFE -42.35
Consensus MFE -30.40
Energy contribution -30.77
Covariance contribution 0.37
Combinations/Pair 1.21
Mean z-score -3.29
Structure conservation index 0.72
SVM decision value 1.07
SVM RNA-class probability 0.910684
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099466 108 - 23771897
UACCCACUCCCCACCGCUGUCGCUGGCAUUUUUCCUUUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGC------GGUGGCGCUGGCGUU
.(((((....((((((((((((((((((.(((...........))).))))))))))...........(((((((.....)))))--))...)))------)))))...))).)). ( -48.30)
>DroSec_CAF1 85479 102 - 1
------CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGC------GGUGGUGCUGGCGUU
------....((((((((((((((((((.(((...........))).))))))))))...........(((((((.....)))))--))...)))------))))).......... ( -45.70)
>DroSim_CAF1 91957 102 - 1
------CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGC------GGUGGUGCUGGCGUU
------....((((((((((((((((((.(((...........))).))))))))))...........(((((((.....)))))--))...)))------))))).......... ( -45.70)
>DroEre_CAF1 84735 99 - 1
------CUCCUCACCGCUGUCGUUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGC------GGUGGCGGUAGC---
------(((((((((((((((.((((((.(((...........))).)))))).)))...........(((((((.....)))))--))...)))------))))).)).)).--- ( -37.30)
>DroYak_CAF1 103362 93 - 1
------CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUCAGCUGCAGGAUUAUUGCG--GUGCUAGC------GGUG------GC---
------....(((((((((((.((((((.(((...........))).)))))).)))...........(((((((.....)))))--))...)))------))))------).--- ( -37.50)
>DroPer_CAF1 104703 113 - 1
--CUCCUUCACUACCAAUGUUGCUGGCAUUUUUCUUCUUUCUUAGAUUGCCAGCGACAUUUCGACUGAGUUGCAGGAUUAUUGUGCGGCA-UGGCUGAGUGUGUGGCACAGGCACG
--.((((.((((...(((((((((((((....(((........))).))))))))))))).......)).)).))))...((((((.(((-(........)))).))))))..... ( -39.60)
>consensus
______CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG__GCGGUGGC______GGUGGCGCUGGCGUU
..........(((((..(((((((((((.(((...........))).)))))))))))...(.((((...(((((.....)))))...)))).).......))))).......... (-30.40 = -30.77 +   0.37) 

alignment

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secondary structure

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Window 8

Location 22,099,498 – 22,099,603
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 73.31
Mean single sequence MFE -32.58
Consensus MFE -16.66
Energy contribution -17.98
Covariance contribution 1.32
Combinations/Pair 1.10
Mean z-score -2.84
Structure conservation index 0.51
SVM decision value 3.52
SVM RNA-class probability 0.999341
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099498 105 + 23771897
CCUGCAGCUCAGUCGAAAUGUCGCUGGCAAUCUAAGGAAAAGGAAAAAUGCCAGCGACAGCGGUGGGGAGUGGGUAGGCGGUGGCGUGCCCCACCAGUCUGUUCA
((..(..((((.(((...(((((((((((.(((........)))....))))))))))).)))))))..)..))((((((((((......))))).))))).... ( -45.70)
>DroPse_CAF1 103583 82 + 1
CCUGCAACUCAGUCGAAAUGUCGCUGGCAAUCUAAGAAAGAAGAAAAAUGCCAGCAACAUUGGUAGUGAAGGAG-----------------------GAGGAGCA
.((.(..(((..(((.(((((.(((((((.(((........)))....))))))).))))).....)))..)))-----------------------..).)).. ( -25.70)
>DroEre_CAF1 84764 95 + 1
CCUGCAGCUCAGUCGAAAUGUCUCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAACGACAGCGGUGAGGAG----------CUGGCGUGCCCCACCAGUCAGUUCA
.......((((.(((...((((..(((((.(((........)))....)))))..)))).)))))))(((----------((((((((...)))..)))))))). ( -30.00)
>DroYak_CAF1 103385 95 + 1
CCUGCAGCUGAGUCGAAAUGUCUCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG----------AUGGCGUGCCCCACCAGUCAGUUCA
...(.((((((...(...((((.((((((.(((........)))....)))))).)))).)(((((((.(----------....)...)))))))..))))))). ( -35.80)
>DroPer_CAF1 104742 82 + 1
CCUGCAACUCAGUCGAAAUGUCGCUGGCAAUCUAAGAAAGAAGAAAAAUGCCAGCAACAUUGGUAGUGAAGGAG-----------------------GAGGAGCA
.((.(..(((..(((.(((((.(((((((.(((........)))....))))))).))))).....)))..)))-----------------------..).)).. ( -25.70)
>consensus
CCUGCAGCUCAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG_G_G_______UGGCGUGCCCCACCAGUCAGUUCA
.......(((..(((...(((((((((((.(((........)))....))))))))))).)))..)))..................................... (-16.66 = -17.98 +   1.32) 

alignment

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secondary structure

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Window 9

Location 22,099,498 – 22,099,603
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 73.31
Mean single sequence MFE -28.93
Consensus MFE -19.09
Energy contribution -22.01
Covariance contribution 2.92
Combinations/Pair 1.12
Mean z-score -2.46
Structure conservation index 0.66
SVM decision value 2.95
SVM RNA-class probability 0.997863
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099498 105 - 23771897
UGAACAGACUGGUGGGGCACGCCACCGCCUACCCACUCCCCACCGCUGUCGCUGGCAUUUUUCCUUUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGG
....(((...(((((((....................)))))))..(((((((((((.(((...........))).)))))))))))......)))......... ( -35.85)
>DroPse_CAF1 103583 82 - 1
UGCUCCUC-----------------------CUCCUUCACUACCAAUGUUGCUGGCAUUUUUCUUCUUUCUUAGAUUGCCAGCGACAUUUCGACUGAGUUGCAGG
(((..(((-----------------------.............(((((((((((((....(((........))).)))))))))))))......)))..))).. ( -25.11)
>DroEre_CAF1 84764 95 - 1
UGAACUGACUGGUGGGGCACGCCAG----------CUCCUCACCGCUGUCGUUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUGAGCUGCAGG
....(((...((((.....))))((----------(((........((((.((((((.(((...........))).)))))).))))........))))).))). ( -27.19)
>DroYak_CAF1 103385 95 - 1
UGAACUGACUGGUGGGGCACGCCAU----------CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUCAGCUGCAGG
((..((((..(((((((........----------..)))))))..((((.((((((.(((...........))).)))))).)))).......))))...)).. ( -31.40)
>DroPer_CAF1 104742 82 - 1
UGCUCCUC-----------------------CUCCUUCACUACCAAUGUUGCUGGCAUUUUUCUUCUUUCUUAGAUUGCCAGCGACAUUUCGACUGAGUUGCAGG
(((..(((-----------------------.............(((((((((((((....(((........))).)))))))))))))......)))..))).. ( -25.11)
>consensus
UGAACCGACUGGUGGGGCACGCCA_______C_C_CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGG
..........(((((((....................)))))))..(((((((((((.(((...........))).)))))))))))......(((.....))). (-19.09 = -22.01 +   2.92) 

alignment

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secondary structure

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dotplot

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Window 0

Location 22,099,536 – 22,099,637
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 70.09
Mean single sequence MFE -34.90
Consensus MFE -18.80
Energy contribution -21.72
Covariance contribution 2.92
Combinations/Pair 1.05
Mean z-score -2.67
Structure conservation index 0.54
SVM decision value 3.33
SVM RNA-class probability 0.999015
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099536 101 + 23771897
AAAGGAAAAAUGCCAGCGACAGCGGUGGGGAGUGGGUAGGCGGUGGCGUGCCCCACCAGUCUGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAAC
...((.......))((((((((((((..((.(.(((((.((....)).)))))).)).(((((((..(((.....)))))))))))))))))))))).... ( -45.90)
>DroPse_CAF1 103621 78 + 1
AGAAGAAAAAUGCCAGCAACAUUGGUAGUGAAGGAG-----------------------GAGGAGCAUCUUCUGGAGCAGCAUCUGCUGCUGUCGCUCCAA
.....................((((.(((((.((((-----------------------((......))))))..((((((....)))))).))))))))) ( -24.70)
>DroEre_CAF1 84802 91 + 1
AGAGGAAAAAUGCCAACGACAGCGGUGAGGAG----------CUGGCGUGCCCCACCAGUCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAAC
.((((........)..(((((((((((.....----------(((.(.(((.((((((((.......)))))))).))))))).))))))))))))))... ( -37.70)
>DroYak_CAF1 103423 91 + 1
AGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG----------AUGGCGUGCCCCACCAGUCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAAC
...((.......))(((((((((((((.....----------...((.(((.((((((((.......)))))))).)))))...))))))))))))).... ( -41.50)
>DroPer_CAF1 104780 78 + 1
AGAAGAAAAAUGCCAGCAACAUUGGUAGUGAAGGAG-----------------------GAGGAGCAUCUUCUGGAGCAGCAUCUGCUGCUGUCGCUCCAA
.....................((((.(((((.((((-----------------------((......))))))..((((((....)))))).))))))))) ( -24.70)
>consensus
AGAGGAAAAAUGCCAGCGACAGCGGUGGGGAG_G_G_______UGGCGUGCCCCACCAGUCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAAC
..............((((((................................((((((((.......))))))))((((((....)))))))))))).... (-18.80 = -21.72 +   2.92) 

alignment

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secondary structure

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dotplot

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Window 1

Location 22,099,536 – 22,099,637
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 70.09
Mean single sequence MFE -32.80
Consensus MFE -20.24
Energy contribution -22.16
Covariance contribution 1.92
Combinations/Pair 1.15
Mean z-score -3.12
Structure conservation index 0.62
SVM decision value 4.01
SVM RNA-class probability 0.999756
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099536 101 - 23771897
GUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACAGACUGGUGGGGCACGCCACCGCCUACCCACUCCCCACCGCUGUCGCUGGCAUUUUUCCUUU
(((.((((((((((((....)))((((((((((((....)).))))))))))..........................))))))))))))........... ( -42.70)
>DroPse_CAF1 103621 78 - 1
UUGGAGCGACAGCAGCAGAUGCUGCUCCAGAAGAUGCUCCUC-----------------------CUCCUUCACUACCAAUGUUGCUGGCAUUUUUCUUCU
....((((((((((((....)))))....((((..(......-----------------------)..))))........))))))).............. ( -20.00)
>DroEre_CAF1 84802 91 - 1
GUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCAG----------CUCCUCACCGCUGUCGUUGGCAUUUUUCCUCU
((..(.((((((((((....)))(((((((((((......).)))))))))).......----------.........))))))))..))........... ( -39.70)
>DroYak_CAF1 103423 91 - 1
GUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCAU----------CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCU
(((.((((((((((((....)))(((((((((((......).)))))))))).......----------.........))))))))))))........... ( -41.60)
>DroPer_CAF1 104780 78 - 1
UUGGAGCGACAGCAGCAGAUGCUGCUCCAGAAGAUGCUCCUC-----------------------CUCCUUCACUACCAAUGUUGCUGGCAUUUUUCUUCU
....((((((((((((....)))))....((((..(......-----------------------)..))))........))))))).............. ( -20.00)
>consensus
GUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACCGACUGGUGGGGCACGCCA_______C_C_CUCCCCACCGCUGUCGCUGGCAUUUUUCCUCU
....((((((((((((....))))).((((((((......).)))))))...............................))))))).............. (-20.24 = -22.16 +   1.92) 

alignment

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secondary structure

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dotplot

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Window 2

Location 22,099,574 – 22,099,669
Length 95
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 77.59
Mean single sequence MFE -27.14
Consensus MFE -16.20
Energy contribution -16.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.60
SVM decision value 0.83
SVM RNA-class probability 0.861409
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099574 95 + 23771897
GGCGGUGGCGUGCCCCACCAGUCUGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAACCACCCACUUCCA--CCUCCUCAACUCCUCCGCCG
(((((.((.((...(((((((.((....)))))))))((((((....))))))......................--........)).)).))))). ( -39.50)
>DroSec_CAF1 85581 76 + 1
---------------------UCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAACCACCCACUUCCACACCUCCUCCACUCCUCCGCCG
---------------------...........(((((((((((....)))))((.....)).............................)))))). ( -17.40)
>DroSim_CAF1 92059 76 + 1
---------------------UCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAACCACCCACUUCCACACCUCCUCCACUCCGCCGCCG
---------------------........((.(((((((((((....)))))((.....))..........................)))))))).. ( -18.70)
>DroEre_CAF1 84834 92 + 1
----CUGGCGUGCCCCACCAGUCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAACCACCCACUUCCACACCUCGUACACCACAUCC-CC
----.(((.((((.((((((((.......))))))))((((((....))))))............................)))).))).....-.. ( -31.30)
>DroYak_CAF1 103455 85 + 1
----AUGGCGUGCCCCACCAGUCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAACCACCCACUUCCACACCUCGUCCACCG--------
----.(((.(((..((((((((.......))))))))((((((....))))))..........))))))....................-------- ( -28.80)
>consensus
_____UGGCGUGCCCCACCAGUCAGUUCAGCUGGUGGAGCAGCAGAUGCUGCUGUCGCUCAACCACCCACUUCCACACCUCCUCCACUCCUCCGCCG
................................(((((((((((....))))))(.....)..))))).............................. (-16.20 = -16.20 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 3

Location 22,099,574 – 22,099,669
Length 95
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 77.59
Mean single sequence MFE -34.98
Consensus MFE -20.18
Energy contribution -20.88
Covariance contribution 0.70
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.58
SVM decision value 0.34
SVM RNA-class probability 0.697214
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22099574 95 - 23771897
CGGCGGAGGAGUUGAGGAGG--UGGAAGUGGGUGGUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACAGACUGGUGGGGCACGCCACCGCC
((((......)))).((.((--(((.((..((((((((.....))))..))))..))((((((((((((....)).))))))))))...))))).)) ( -44.50)
>DroSec_CAF1 85581 76 - 1
CGGCGGAGGAGUGGAGGAGGUGUGGAAGUGGGUGGUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGA---------------------
((((((.((((..(...((((((....((..((.(.....).)).)).)))))).)..)))).)).))))......--------------------- ( -27.20)
>DroSim_CAF1 92059 76 - 1
CGGCGGCGGAGUGGAGGAGGUGUGGAAGUGGGUGGUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGA---------------------
((((((.((((..(...((((((....((..((.(.....).)).)).)))))).)..)))).)).))))......--------------------- ( -28.00)
>DroEre_CAF1 84834 92 - 1
GG-GGAUGUGGUGUACGAGGUGUGGAAGUGGGUGGUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCAG----
..-.....((((((............((..((((((((.....))))..))))..))(((((((((((......).)))))))))))))))).---- ( -37.80)
>DroYak_CAF1 103455 85 - 1
--------CGGUGGACGAGGUGUGGAAGUGGGUGGUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCAU----
--------((.....)).(((((...((..((((((((.....))))..))))..))(((((((((((......).)))))))))))))))..---- ( -37.40)
>consensus
CGGCGGAGGAGUGGAGGAGGUGUGGAAGUGGGUGGUUGAGCGACAGCAGCAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCA_____
.....................((...(((.(((((.........((((((....))))))))))).)))..))....(((((.....)))))..... (-20.18 = -20.88 +   0.70) 

alignment

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secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:38 2006