Locus 6036

Sequence ID 2R_DroMel_CAF1
Location 18,993,774 – 18,993,898
Length 124
Max. P 0.818344
window9673 window9674 window9675 window9676

overview

Window 3

Location 18,993,774 – 18,993,868
Length 94
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 77.77
Mean single sequence MFE -25.93
Consensus MFE -12.39
Energy contribution -13.01
Covariance contribution 0.61
Combinations/Pair 1.24
Mean z-score -2.11
Structure conservation index 0.48
SVM decision value 0.37
SVM RNA-class probability 0.709326
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18993774 94 + 20766785
AGUGCAACAGUGCUCUUUUUUGUGC-C-------ACACACGCA--CAGCAAUUAUCGCUGCUUCUC--------GCGUUCAUCAGGCACUUUGGCAGCAGCCAGCUGCUAAG
((..(....)..)).......((((-(-------....((((.--.((((........))))....--------))))......))))).((((((((.....)))))))). ( -28.70)
>DroSec_CAF1 91928 86 + 1
----------UGCUCCUUUUUGUGC-C-------ACACACGCACACAGCAAUUAUCGCUGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAG
----------..........(((((-.-------......)))))((((.......))))......--------((((.....))))...((((((((.....)))))))). ( -25.00)
>DroSim_CAF1 96846 86 + 1
----------UGCUCUUUUUUGUGC-C-------ACACACGCACACAGCAAUUAUCGCUGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAG
----------..........(((((-.-------......)))))((((.......))))......--------((((.....))))...((((((((.....)))))))). ( -25.00)
>DroEre_CAF1 94754 84 + 1
----------UGCUCUUUUUUGUGC-C-------ACACACGCA--CAGCAAUUAUCGCCGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCGGCUGCCAAG
----------.((.......(((((-.-------......)))--))((.......)).)).....--------((((.....))))...((((((((.....)))))))). ( -24.90)
>DroWil_CAF1 125269 100 + 1
----------AAUUCGUUUGUGUGUGUAUAGAGAAUAGAGUCG--AAACAAUUAUCGCUGAUUCGCCGACUGCUCUCGCAGUCACGCACUUUGACUGCAGCCAGAUGCUGAA
----------.....(((...((((((.....((((..((.((--(........))))).))))...((((((....))))))))))))...)))..((((.....)))).. ( -29.30)
>DroYak_CAF1 95154 84 + 1
----------UGCUCUUUUUUGUGC-C-------ACACACGCA--CAGCAAUUAUCGCCGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAG
----------.((.......(((((-.-------......)))--))((.......)).)).....--------((((.....))))...((((((((.....)))))))). ( -22.70)
>consensus
__________UGCUCUUUUUUGUGC_C_______ACACACGCA__CAGCAAUUAUCGCUGCUUCUC________GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAG
.....................((((...............((.....))......(((................)))........)))).((((((((.....)))))))). (-12.39 = -13.01 +   0.61)

alignment

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secondary structure

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Window 4

Location 18,993,774 – 18,993,868
Length 94
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.77
Mean single sequence MFE -29.55
Consensus MFE -13.78
Energy contribution -13.01
Covariance contribution -0.77
Combinations/Pair 1.36
Mean z-score -1.97
Structure conservation index 0.47
SVM decision value -0.05
SVM RNA-class probability 0.509624
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18993774 94 - 20766785
CUUAGCAGCUGGCUGCUGCCAAAGUGCCUGAUGAACGC--------GAGAAGCAGCGAUAAUUGCUG--UGCGUGUGU-------G-GCACAAAAAAGAGCACUGUUGCACU
....(((((((((....))))..(((((......((((--------(....(((((((...))))))--).)))))..-------)-)))).............)))))... ( -35.70)
>DroSec_CAF1 91928 86 - 1
CUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCAGCGAUAAUUGCUGUGUGCGUGUGU-------G-GCACAAAAAGGAGCA----------
..((((((....))))))((....((.((.(((.((((--------(....(((((((...))))))).))))).)))-------.-)).))....))....---------- ( -28.70)
>DroSim_CAF1 96846 86 - 1
CUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCAGCGAUAAUUGCUGUGUGCGUGUGU-------G-GCACAAAAAAGAGCA----------
....((.((((((....))))....))(((....((((--------(....(((((((...)))))))...)))))..-------.-.)))........)).---------- ( -28.40)
>DroEre_CAF1 94754 84 - 1
CUUGGCAGCCGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCGGCGAUAAUUGCUG--UGCGUGUGU-------G-GCACAAAAAAGAGCA----------
.((((((((.....)))))))).....(((....((((--------(....(((((((...))))))--).)))))..-------.-.)))...........---------- ( -31.00)
>DroWil_CAF1 125269 100 - 1
UUCAGCAUCUGGCUGCAGUCAAAGUGCGUGACUGCGAGAGCAGUCGGCGAAUCAGCGAUAAUUGUUU--CGACUCUAUUCUCUAUACACACACAAACGAAUU----------
..((((.....))))........(((.((((((((....))))))((.((((.(((((........)--)).))..)))).))....)).))).........---------- ( -26.40)
>DroYak_CAF1 95154 84 - 1
CUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCGGCGAUAAUUGCUG--UGCGUGUGU-------G-GCACAAAAAAGAGCA----------
....((.((((((....))))....))(((....((((--------(....(((((((...))))))--).)))))..-------.-.)))........)).---------- ( -27.10)
>consensus
CUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC________GAGAAGCAGCGAUAAUUGCUG__UGCGUGUGU_______G_GCACAAAAAAGAGCA__________
(((.(((((.....)))))....((((.......((((..............((((((...)))))).....))))...........))))......)))............ (-13.78 = -13.01 +  -0.77)

alignment

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secondary structure

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Window 5

Location 18,993,800 – 18,993,898
Length 98
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 81.98
Mean single sequence MFE -26.28
Consensus MFE -20.59
Energy contribution -20.65
Covariance contribution 0.06
Combinations/Pair 1.27
Mean z-score -1.91
Structure conservation index 0.78
SVM decision value 0.67
SVM RNA-class probability 0.818344
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18993800 98 + 20766785
ACACACGCA--CAGCAAUUAUCGCUGCUUCUC--------GCGUUCAUCAGGCACUUUGGCAGCAGCCAGCUGCUAAGUAACUUCAUUUGACUUGGCUACACGCCAAA------
....((((.--.((((........))))....--------))))(((..((..((((.((((((.....))))))))))..)).....))).(((((.....))))).------ ( -26.30)
>DroSec_CAF1 91944 100 + 1
ACACACGCACACAGCAAUUAUCGCUGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAGUAACUUCAUUUGACUUGGCUACACGCCAAA------
...........((((.......))))......--------((((.....))))((((.((((((.....)))))))))).............(((((.....))))).------ ( -26.40)
>DroSim_CAF1 96862 100 + 1
ACACACGCACACAGCAAUUAUCGCUGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAGUAACUUCAUUUGACUUGGCUACACGCCAAA------
...........((((.......))))......--------((((.....))))((((.((((((.....)))))))))).............(((((.....))))).------ ( -26.40)
>DroEre_CAF1 94770 104 + 1
ACACACGCA--CAGCAAUUAUCGCCGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCGGCUGCCAAGUAACUUCAUUUGACUUGGCUGCACGCCAAAGCCAAA
......((.--..((.......)).)).....--------((((.....)))).(((((((.(((((((...(.(((((......))))).).)))))))..)))))))..... ( -29.60)
>DroYak_CAF1 95170 98 + 1
ACACACGCA--CAGCAAUUAUCGCCGCUUCUC--------GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAGUAACUUCAUUUGACUUGGCUACACGCCAAA------
......((.--..((.......)).)).....--------((((.....))))((((.((((((.....)))))))))).............(((((.....))))).------ ( -23.50)
>DroPer_CAF1 96252 112 + 1
AGAUAUAGA--CAACAAUUAUCUUUGAUUCUCGCUCUGCUGCGUCAGUCACGCACUUUGACGGCACAGAGAUGCUAAAUAACUUAAUUUUCUGUUGCUGCAUGCUGCAUAGAGG
(((((....--.......))))).(((((..(((......)))..))))).(((...((.(((((((((((...(((.....)))..)))))).)))))))...)))....... ( -25.50)
>consensus
ACACACGCA__CAGCAAUUAUCGCUGCUUCUC________GCGUUCAUCACGCACUUUGGCAGCAGCCAGCUGCUAAGUAACUUCAUUUGACUUGGCUACACGCCAAA______
...........((((.......))))..............((((.....))))..(((((((((.....)))))))))..............(((((.....)))))....... (-20.59 = -20.65 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,993,800 – 18,993,898
Length 98
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 81.98
Mean single sequence MFE -33.32
Consensus MFE -21.29
Energy contribution -21.85
Covariance contribution 0.56
Combinations/Pair 1.21
Mean z-score -1.75
Structure conservation index 0.64
SVM decision value 0.09
SVM RNA-class probability 0.580050
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18993800 98 - 20766785
------UUUGGCGUGUAGCCAAGUCAAAUGAAGUUACUUAGCAGCUGGCUGCUGCCAAAGUGCCUGAUGAACGC--------GAGAAGCAGCGAUAAUUGCUG--UGCGUGUGU
------(((((((.(((((((.((....(((......)))...))))))))))))))))...........((((--------(....(((((((...))))))--).))))).. ( -34.00)
>DroSec_CAF1 91944 100 - 1
------UUUGGCGUGUAGCCAAGUCAAAUGAAGUUACUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCAGCGAUAAUUGCUGUGUGCGUGUGU
------(((((((.(((((((.((....(((......)))...))))))))))))))))...........((((--------(....(((((((...)))))))...))))).. ( -34.60)
>DroSim_CAF1 96862 100 - 1
------UUUGGCGUGUAGCCAAGUCAAAUGAAGUUACUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCAGCGAUAAUUGCUGUGUGCGUGUGU
------(((((((.(((((((.((....(((......)))...))))))))))))))))...........((((--------(....(((((((...)))))))...))))).. ( -34.60)
>DroEre_CAF1 94770 104 - 1
UUUGGCUUUGGCGUGCAGCCAAGUCAAAUGAAGUUACUUGGCAGCCGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCGGCGAUAAUUGCUG--UGCGUGUGU
....(((((((((.((((((..(((((..........)))))....))))))))))))))).........((((--------(....(((((((...))))))--).))))).. ( -40.90)
>DroYak_CAF1 95170 98 - 1
------UUUGGCGUGUAGCCAAGUCAAAUGAAGUUACUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC--------GAGAAGCGGCGAUAAUUGCUG--UGCGUGUGU
------(((((((.(((((((.((....(((......)))...))))))))))))))))...........((((--------(....(((((((...))))))--).))))).. ( -33.30)
>DroPer_CAF1 96252 112 - 1
CCUCUAUGCAGCAUGCAGCAACAGAAAAUUAAGUUAUUUAGCAUCUCUGUGCCGUCAAAGUGCGUGACUGACGCAGCAGAGCGAGAAUCAAAGAUAAUUGUUG--UCUAUAUCU
......(((.....)))(((((((.((((......)))).((.(((((((((.((((.......)))).).))))).)))))...............))))))--)........ ( -22.50)
>consensus
______UUUGGCGUGUAGCCAAGUCAAAUGAAGUUACUUAGCAGCUGGCUGCUGCCAAAGUGCGUGAUGAACGC________GAGAAGCAGCGAUAAUUGCUG__UGCGUGUGU
......(((((((.(((((((..((....)).(((....)))...))))))))))))))..((((.....))))..............((((((...))))))........... (-21.29 = -21.85 +   0.56)

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 12:00:57 2006