Locus 1603

Sequence ID 2L_DroMel_CAF1
Location 4,304,739 – 4,304,894
Length 155
Max. P 0.834905
window2571 window2572 window2573

overview

Window 1

Location 4,304,739 – 4,304,858
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.11
Mean single sequence MFE -36.68
Consensus MFE -34.00
Energy contribution -33.42
Covariance contribution -0.58
Combinations/Pair 1.10
Mean z-score -1.17
Structure conservation index 0.93
SVM decision value 0.46
SVM RNA-class probability 0.743998
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4304739 119 + 22407834
CGGCACGAGGACAUCGGAGAGUACACUUGCAUUGCACGCAAUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUCGCGGGCGGCGCUGUAAUCAUGGUAAAAACCUAAAUA-CA
.((..(((.....))).....(((...((.(((((((((....(((.((((......)))).))).(((((((.......))))))).))).))))))))..)))....))......-.. ( -36.80)
>DroVir_CAF1 36344 119 + 1
CGGCACGAGGAUAUCGGAGAAUACACUUGCAUUGCACGCAAUGGUGAGGGACAGGUCUCCCAUACGGCCCGCGUUAUAAUUGCGGGCGGCGCUGUAAUAAUGGUAAAAACCUAUAAA-CA
..((.(((.....)))(((......)))))(((((((((....(((.((((......)))).))).(((((((.......))))))).))).))))))...(((....)))......-.. ( -36.70)
>DroGri_CAF1 50529 120 + 1
CGGCACGAGGACAUCGGCGAAUACACUUGUAUUGCACGCAAUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUUGCGGGCGGCGCUGUAAUCAUGGUAAAAACCUAUAAAACA
..((.(((.....)))))...(((...((.(((((((((....(((.((((......)))).))).(((((((.......))))))).))).))))))))..)))............... ( -36.50)
>DroWil_CAF1 69195 114 + 1
CGCCACGAGGAUAUCGGGGAAUAUACUUGCAUUGCACGCAAUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUUGCGGGCGGCGCUGUAAUCAUGGUAAAAACCCUA------
.....(((.....)))(((....((((((.(((((((((....(((.((((......)))).))).(((((((.......))))))).))).)))))))).))))....)))..------ ( -38.00)
>DroMoj_CAF1 42815 119 + 1
CGCCACGAGGACAUCGGAGAAUACACUUGCAUUGCACGCAAUGGUGAGGGACAAGUCUCCCAUACGGCCCGCGUUAUAAUUGCGGGCGGCGCUGUAAUAAUGGUAAAAACCUAUAAA-CA
.(((((((.....)))..............(((((((((....(((.((((......)))).))).(((((((.......))))))).))).))))))..)))).............-.. ( -37.30)
>DroAna_CAF1 39217 115 + 1
CGGCACGAGGACAUCGGAGAGUACACUUGCAUUGCACGCAAUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUCGCGGGUGGCGCUGUAAUCAUGGUAAAAACCUAAA-----
.((..(((.....))).....(((...((.(((((((((....(((.((((......)))).))).(((((((.......))))))).))).))))))))..)))....))....----- ( -34.80)
>consensus
CGGCACGAGGACAUCGGAGAAUACACUUGCAUUGCACGCAAUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUUGCGGGCGGCGCUGUAAUCAUGGUAAAAACCUAAAAA_CA
.....(((.....)))........(((...(((((((((....(((.((((......)))).))).(((((((.......))))))).))).))))))...)))................ (-34.00 = -33.42 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,304,779 – 4,304,894
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.84
Mean single sequence MFE -27.05
Consensus MFE -25.26
Energy contribution -24.68
Covariance contribution -0.58
Combinations/Pair 1.14
Mean z-score -1.39
Structure conservation index 0.93
SVM decision value 0.73
SVM RNA-class probability 0.834905
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4304779 115 + 22407834
AUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUCGCGGGCGGCGCUGUAAUCAUGGUAAAAACCUAAAUA-CAAA-UCACUUAAU--UUUGA-GAUACAUAAGGGGCUGUCCC
.......((((((.(((((.....(.(((((((.......))))))).)...((((.((..(((....)))......-((((-.........--)))).-))))))...))))))))))) ( -34.60)
>DroVir_CAF1 36384 102 + 1
AUGGUGAGGGACAGGUCUCCCAUACGGCCCGCGUUAUAAUUGCGGGCGGCGCUGUAAUAAUGGUAAAAACCUAUAAA-CAAA-UCAAUUAUA--UACCA-GAUAA----UC---------
.(((((.((((......))))...(.(((((((.......))))))).)...(((......(((....))).....)-))..-.........--)))))-.....----..--------- ( -27.20)
>DroGri_CAF1 50569 106 + 1
AUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUUGCGGGCGGCGCUGUAAUCAUGGUAAAAACCUAUAAAACAAA-UCAAUUAUAAUUAUCA-GAUAA----UCC--------
((((((.((((......))))...(.(((((((.......))))))).))))))).(((.((((((.....(((((......-....))))).))))))-)))..----...-------- ( -24.30)
>DroWil_CAF1 69235 93 + 1
AUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUUGCGGGCGGCGCUGUAAUCAUGGUAAAAACCCUA-------A-UUACUUAAA---UUGA-GAUUA---------------
..((((.((((......))))...(.(((((((.......))))))).)))))(((((...(((....)))...-------)-)))).....---....-.....--------------- ( -25.30)
>DroMoj_CAF1 42855 104 + 1
AUGGUGAGGGACAAGUCUCCCAUACGGCCCGCGUUAUAAUUGCGGGCGGCGCUGUAAUAAUGGUAAAAACCUAUAAA-CAAACUGAACUAUU--UACGAAAAUAA----UC---------
((((((.((((......))))...(.(((((((.......))))))).)))))))......(((....)))......-..............--...........----..--------- ( -26.00)
>DroAna_CAF1 39257 100 + 1
AUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUCGCGGGUGGCGCUGUAAUCAUGGUAAAAACCUAAA--------CUACAUUAU--UUUGA-GACACAUUAAG---------
...(((.((((......))))...(.(((((((.......))))))).)...((((.....(((....)))....--------.))))....--.....-..)))......--------- ( -24.90)
>consensus
AUGGUGAGGGACAAGUCUCCCAUACGGCCCGUGUUAUAAUUGCGGGCGGCGCUGUAAUCAUGGUAAAAACCUAAAAA_CAAA_UCAAUUAAA__UAUGA_GAUAA____UC_________
((((((.((((......))))...(.(((((((.......))))))).)))))))......(((....)))................................................. (-25.26 = -24.68 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,304,779 – 4,304,894
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.84
Mean single sequence MFE -26.30
Consensus MFE -17.78
Energy contribution -17.95
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.68
SVM decision value 0.40
SVM RNA-class probability 0.722969
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4304779 115 - 22407834
GGGACAGCCCCUUAUGUAUC-UCAAA--AUUAAGUGA-UUUG-UAUUUAGGUUUUUACCAUGAUUACAGCGCCGCCCGCGAUUAUAACACGGGCCGUAUGGGAGACUUGUCCCUCACCAU
(((((((((((.((((....-.....--.....(((.-..((-((.((((((....))).))).)))).))).(((((.(.......).))))))))).))).).).))))))....... ( -35.20)
>DroVir_CAF1 36384 102 - 1
---------GA----UUAUC-UGGUA--UAUAAUUGA-UUUG-UUUAUAGGUUUUUACCAUUAUUACAGCGCCGCCCGCAAUUAUAACGCGGGCCGUAUGGGAGACCUGUCCCUCACCAU
---------..----.....-((((.--.((((....-.)))-)..(((((((((..((((.......(((..((((((.........)))))))))))))))))))))).....)))). ( -25.91)
>DroGri_CAF1 50569 106 - 1
--------GGA----UUAUC-UGAUAAUUAUAAUUGA-UUUGUUUUAUAGGUUUUUACCAUGAUUACAGCGCCGCCCGCAAUUAUAACACGGGCCGUAUGGGAGACUUGUCCCUCACCAU
--------((.----....(-((.(((((((...(((-......)))..(((....))))))))))))).((.(((((...........))))).))..((((......))))...)).. ( -22.70)
>DroWil_CAF1 69235 93 - 1
---------------UAAUC-UCAA---UUUAAGUAA-U-------UAGGGUUUUUACCAUGAUUACAGCGCCGCCCGCAAUUAUAACACGGGCCGUAUGGGAGACUUGUCCCUCACCAU
---------------.....-....---.....((((-(-------((.(((....))).)))))))...((.(((((...........))))).))(((((((........))).)))) ( -24.90)
>DroMoj_CAF1 42855 104 - 1
---------GA----UUAUUUUCGUA--AAUAGUUCAGUUUG-UUUAUAGGUUUUUACCAUUAUUACAGCGCCGCCCGCAAUUAUAACGCGGGCCGUAUGGGAGACUUGUCCCUCACCAU
---------..----........(((--(((((......)))-))))).(((....)))...........((.((((((.........)))))).))(((((((........))).)))) ( -25.90)
>DroAna_CAF1 39257 100 - 1
---------CUUAAUGUGUC-UCAAA--AUAAUGUAG--------UUUAGGUUUUUACCAUGAUUACAGCGCCACCCGCGAUUAUAACACGGGCCGUAUGGGAGACUUGUCCCUCACCAU
---------......((.((-(((..--....(((((--------((..(((....)))..)))))))(((...((((.(.......).)))).))).))))).)).............. ( -23.20)
>consensus
_________GA____UUAUC_UCAAA__AAUAAGUGA_UUUG_UUUAUAGGUUUUUACCAUGAUUACAGCGCCGCCCGCAAUUAUAACACGGGCCGUAUGGGAGACUUGUCCCUCACCAU
.................................................(((....))).........(((..(((((...........))))))))(((((((........))).)))) (-17.78 = -17.95 +   0.17)

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 10:06:25 2006