Locus 5992

Sequence ID 3L_DroMel_CAF1
Location 16,005,899 – 16,006,144
Length 245
Max. P 0.987079
window9581 window9582 window9583 window9584 window9585

overview

Window 1

Location 16,005,899 – 16,006,008
Length 109
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 80.76
Mean single sequence MFE -29.48
Consensus MFE -18.09
Energy contribution -18.29
Covariance contribution 0.20
Combinations/Pair 1.25
Mean z-score -2.65
Structure conservation index 0.61
SVM decision value 1.07
SVM RNA-class probability 0.909854
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16005899 109 + 23771897
GCUAAGGGUGGUUUUUCCCUUC----GGGAAAAACUCCCGAG--UUGCGACUACAAAAAAAAAAAAAAAACAAAUAUUCGUAGUGCCAUCGAAUACGCAAUGUUACAACCGCUAC
((...(((.((((((((((...----)))))))))))))..(--(((((.........................((((((.........)))))))))))).........))... ( -26.41)
>DroSec_CAF1 6215 98 + 1
GCCAAGGGUGGUUUUUCCUUUC----GGGAAAAACUCCCGAG--UUGCGACUACAAAACAA-----------AAUAUUCGUAGUGCCAUCGAGUACGCAAUGUUACAACCGCUCG
.....((((((((.......((----((((.....))))))(--((((((((((.......-----------.......)))))((......)).)))))).....)))))))). ( -29.54)
>DroSim_CAF1 13955 98 + 1
GCCAAGGGUGGUUUUUCCUUUC----GGGAAAAACUCCCGAG--UUGCGACUACAAAACAA-----------AAUAUUCGUAGUGCCAUCGAGUACGCAAUGUUACAACCGCUCG
.....((((((((.......((----((((.....))))))(--((((((((((.......-----------.......)))))((......)).)))))).....)))))))). ( -29.54)
>DroEre_CAF1 7662 94 + 1
GCCAAGGGUGGUUUUUCCUUUC----GGGAAAAACUGCCGAG--UUGCGACUGAAA----A-----------AAUAUUCGUAGUGCCAUAGAGUACGCAAUGUUACAACCGCUCG
((....((..((((((((....----.))))))))..))(.(--(((..((.(((.----.-----------....)))((.((((......))))))...))..)))))))... ( -27.90)
>DroYak_CAF1 30686 94 + 1
GCCAAGGGUGGUUUUUCCUUUC----GGGAAAAACUCCCGAG--CUGCGACUGAAA----A-----------AGUAUUCGUAGUGCCAUAGAGUACGCAAUGUUACAACCGCUCG
.....(((.(((((((((....----.))))))))))))(((--(((..((.....----.-----------.((((((...........)))))).....))..))...)))). ( -29.00)
>DroAna_CAF1 6345 108 + 1
UCCGAGGGUGGUUUUUCAUUUUCCGAAGGAAAAACUCCCUCGGAAAAUGACAAAAAAAAAA---AAAAUA---GAAAUCGUAGUGU-AUAGAGUACGCAAUAUUACAACCACUCG
.....((((((((..(((((((((((.(((.....))).)))))))))))...........---......---.........((((-((...))))))........)))))))). ( -34.50)
>consensus
GCCAAGGGUGGUUUUUCCUUUC____GGGAAAAACUCCCGAG__UUGCGACUAAAAAA_AA___________AAUAUUCGUAGUGCCAUAGAGUACGCAAUGUUACAACCGCUCG
.....((((((((((((((.......)))))).((((.......((((((...........................)))))).......))))............)))))))). (-18.09 = -18.29 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,006,008 – 16,006,112
Length 104
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 77.46
Mean single sequence MFE -29.33
Consensus MFE -21.26
Energy contribution -22.26
Covariance contribution 1.00
Combinations/Pair 1.16
Mean z-score -1.77
Structure conservation index 0.72
SVM decision value 0.83
SVM RNA-class probability 0.861402
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16006008 104 + 23771897
UUUUUCCAGUGCGCAGAAUCGCAGUGAGUAUUAGUAUCAAAUCCUAAUCCUAUCCAAAACAGCACCACCA-------AAGGCAAAGCUAAGUGGGUGGUGGUGUUUCCUUU
......((.((((......)))).))((.(((((.........))))).)).....(((((.(((((((.-------..(((...))).....))))))).)))))..... ( -27.60)
>DroSec_CAF1 6313 96 + 1
UUUUCCCAGUGCGCCGAAUCGCAGUGAGUAUUAGUAU-----CCUAAUCG----CAAAACAGCACCACCGG------UAGGCAAAGCUAAGUGGGUGGUGCUGUUUUCUUU
......((.((((......)))).)).(((((((...-----.))))).)----)((((((((((((((.(------..(((...)))...).)))))))))))))).... ( -34.00)
>DroSim_CAF1 14053 96 + 1
UUUUCCCAGUGCGCCGAAUCGCAGUGAGUAUUAGUAU-----CCUAAUCG----CAAAACAGCACCACCGG------AAGGCAAAGCUAAGUGGGUGGUGCUGUUUUCUUU
......((.((((......)))).)).(((((((...-----.))))).)----)((((((((((((((.(------..(((...)))...).)))))))))))))).... ( -35.10)
>DroEre_CAF1 7756 93 + 1
UUUUCGCAGUGCGCCGAAUCGCAGUGAGUAUUAGUAU-----UCUAUUCU----CAAAACAGCACAGCUUUUGGUGGUAAGCAGUAGUGAGUGGGUGGUGUU---------
..(((((.((((((......))..((((...(((...-----.)))..))----)).....)))).((((........))))....)))))...........--------- ( -20.60)
>consensus
UUUUCCCAGUGCGCCGAAUCGCAGUGAGUAUUAGUAU_____CCUAAUCG____CAAAACAGCACCACCGG______AAGGCAAAGCUAAGUGGGUGGUGCUGUUUUCUUU
......((.((((......)))).))..............................(((((((((((((........................)))))))))))))..... (-21.26 = -22.26 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,006,008 – 16,006,112
Length 104
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 77.46
Mean single sequence MFE -27.12
Consensus MFE -19.61
Energy contribution -22.73
Covariance contribution 3.12
Combinations/Pair 1.04
Mean z-score -2.00
Structure conservation index 0.72
SVM decision value 1.43
SVM RNA-class probability 0.953372
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16006008 104 - 23771897
AAAGGAAACACCACCACCCACUUAGCUUUGCCUU-------UGGUGGUGCUGUUUUGGAUAGGAUUAGGAUUUGAUACUAAUACUCACUGCGAUUCUGCGCACUGGAAAAA
....((((((.(((((((......((...))...-------.))))))).)))))).......(((((.........)))))..(((.((((......)))).)))..... ( -24.40)
>DroSec_CAF1 6313 96 - 1
AAAGAAAACAGCACCACCCACUUAGCUUUGCCUA------CCGGUGGUGCUGUUUUG----CGAUUAGG-----AUACUAAUACUCACUGCGAUUCGGCGCACUGGGAAAA
....((((((((((((((....(((......)))------..)))))))))))))).----..(((((.-----...))))).((((.((((......)))).)))).... ( -35.50)
>DroSim_CAF1 14053 96 - 1
AAAGAAAACAGCACCACCCACUUAGCUUUGCCUU------CCGGUGGUGCUGUUUUG----CGAUUAGG-----AUACUAAUACUCACUGCGAUUCGGCGCACUGGGAAAA
....((((((((((((((......((...))...------..)))))))))))))).----..(((((.-----...))))).((((.((((......)))).)))).... ( -35.10)
>DroEre_CAF1 7756 93 - 1
---------AACACCACCCACUCACUACUGCUUACCACCAAAAGCUGUGCUGUUUUG----AGAAUAGA-----AUACUAAUACUCACUGCGAUUCGGCGCACUGCGAAAA
---------..................................((.((((.....((----((..(((.-----...)))...))))..((......)))))).))..... ( -13.50)
>consensus
AAAGAAAACAGCACCACCCACUUAGCUUUGCCUA______CCGGUGGUGCUGUUUUG____CGAUUAGG_____AUACUAAUACUCACUGCGAUUCGGCGCACUGGGAAAA
....((((((((((((((........................)))))))))))))).......(((((.........))))).((((.((((......)))).)))).... (-19.61 = -22.73 +   3.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,006,044 – 16,006,144
Length 100
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 84.64
Mean single sequence MFE -32.27
Consensus MFE -29.00
Energy contribution -30.00
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.79
Structure conservation index 0.90
SVM decision value 2.07
SVM RNA-class probability 0.987079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16006044 100 + 23771897
UCAAAUCCUAAUCCUAUCCAAAACAGCACCACCA-AAGGCAAAGCUAAGUGGGUGGUGGUGUUUCCUUUUUUUCU----UAGAAAAGUUCGUGGCGCCAGCCAGA
....................(((((.(((((((.-..(((...))).....))))))).))))).(((((((...----.)))))))....((((....)))).. ( -27.80)
>DroSec_CAF1 6349 95 + 1
U-----CCUAAUCG----CAAAACAGCACCACCGGUAGGCAAAGCUAAGUGGGUGGUGCUGUUUUCUUUUU-UUUUCCAUAGAAAAGUCGGUGGCGCCAGCCAGA
.-----((......----.((((((((((((((.(..(((...)))...).))))))))))))))((((((-(.......)))))))..))((((....)))).. ( -33.80)
>DroSim_CAF1 14089 96 + 1
U-----CCUAAUCG----CAAAACAGCACCACCGGAAGGCAAAGCUAAGUGGGUGGUGCUGUUUUCUUUUUUUUUUCUAUAGAAAAGUCGGUGGCGCCAGCCAGA
.-----....((((----(((((((((((((((.(..(((...)))...).)))))))))))))).......(((((....)))))).))))(((....)))... ( -35.20)
>consensus
U_____CCUAAUCG____CAAAACAGCACCACCGGAAGGCAAAGCUAAGUGGGUGGUGCUGUUUUCUUUUUUUUUUC_AUAGAAAAGUCGGUGGCGCCAGCCAGA
...................((((((((((((((....(((...))).....))))))))))))))(((((((........)))))))....((((....)))).. (-29.00 = -30.00 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,006,044 – 16,006,144
Length 100
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 84.64
Mean single sequence MFE -29.38
Consensus MFE -25.79
Energy contribution -25.90
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.88
SVM decision value 1.08
SVM RNA-class probability 0.911697
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16006044 100 - 23771897
UCUGGCUGGCGCCACGAACUUUUCUA----AGAAAAAAAGGAAACACCACCACCCACUUAGCUUUGCCUU-UGGUGGUGCUGUUUUGGAUAGGAUUAGGAUUUGA
((((((....)))).))....(((((----(.........((((((.(((((((......((...))...-.))))))).))))))........))))))..... ( -24.83)
>DroSec_CAF1 6349 95 - 1
UCUGGCUGGCGCCACCGACUUUUCUAUGGAAAA-AAAAAGAAAACAGCACCACCCACUUAGCUUUGCCUACCGGUGGUGCUGUUUUG----CGAUUAGG-----A
..((((....))))((...(((((....)))))-......((((((((((((((....(((......)))..)))))))))))))).----......))-----. ( -31.90)
>DroSim_CAF1 14089 96 - 1
UCUGGCUGGCGCCACCGACUUUUCUAUAGAAAAAAAAAAGAAAACAGCACCACCCACUUAGCUUUGCCUUCCGGUGGUGCUGUUUUG----CGAUUAGG-----A
..((((....))))((...(((((....))))).......((((((((((((((......((...)).....)))))))))))))).----......))-----. ( -31.40)
>consensus
UCUGGCUGGCGCCACCGACUUUUCUAU_GAAAAAAAAAAGAAAACAGCACCACCCACUUAGCUUUGCCUUCCGGUGGUGCUGUUUUG____CGAUUAGG_____A
..((((....))))..........................((((((((((((((......((...)).....))))))))))))))................... (-25.79 = -25.90 +   0.11)

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 12:06:14 2006