Locus 2604

Sequence ID 3R_DroMel_CAF1
Location 7,042,923 – 7,043,074
Length 151
Max. P 0.934236
window4238 window4239 window4240

overview

Window 8

Location 7,042,923 – 7,043,040
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.37
Mean single sequence MFE -30.22
Consensus MFE -16.38
Energy contribution -15.38
Covariance contribution -1.00
Combinations/Pair 1.39
Mean z-score -2.16
Structure conservation index 0.54
SVM decision value 1.23
SVM RNA-class probability 0.934236
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7042923 117 + 27905053
GAAGAAGCAAGAACACGGCCAAAAUAAAGUCCAAGAAGCACACAAUGCGCGUGGGCCGAAAGCUGAUCCAUGUAAAAGUCAUCGAUGAUAAGCAGCCAAAGCGUAUUGUGGACCGCA
......((........((.(........).))........((((((((((...(((.....(((.(((.(((.......))).)))....))).)))...))))))))))....)). ( -29.00)
>DroPse_CAF1 439 116 + 1
GUC-UAACAAAACGAAGGGCAAAAUGAAGGCCAAUAAGCAAACAAUGCGUCUGGGACGAAAACUCAUACACGUCAAGGUGAUUGACGAUGCUAAUCCCAAACGCAUUGUGGAUCGGG
...-........(((..(((.........))).........(((((((((.(((((.((....)).....((((((.....)))))).......))))).)))))))))...))).. ( -34.40)
>DroEre_CAF1 596 117 + 1
GAAGAAUCAAUAACUCGGCCAAAAUCAAAUCCAAGAAGCACACAAUGCGCAUGGGCCGAAAGCUAAUCCAUGUGAAAGUCAUCGAUGAUAAGCAACCAAAGCGUAUUGUGGACCGAA
..............((((.(....((........))....(((((((((((((((.(....)....))))).((...((((....))))...))......))))))))))).)))). ( -26.60)
>DroYak_CAF1 602 117 + 1
GAAGAAUCAAGAACUCGGCCAAAAUCAAAUCCAAGAAGCACACAAUGCGCAUGGGCCGAAAGCUUAUUCAUGUGAAAGUCAUCGAUGAUAAGCAGCCAAAGCGCAUUGUGGACCGAA
..............((((.(....((........))....((((((((((...(((.....((((((.((((((.....)))..))))))))).)))...))))))))))).)))). ( -34.20)
>DroAna_CAF1 374 111 + 1
------GCAAGAUGAAGGUGAAGAAUAAGUCCAAUAAAAAAACGAUGCGCCUGGGCCGAAAGCUGAUUCACGUUAAAGUCAUUGACGACAAACAACCAAAGCGCAUUGUGGACCGGA
------......................((((.........(((((((((.((((.(....)).......((((((.....))))))........)))..))))))))))))).... ( -24.90)
>DroPer_CAF1 613 116 + 1
GUC-AAACAAAACGAAGGGCAAAAUGAAGGCCAAUAAGCAAACAAUGCGCCUGGGACGAAAACUCAUACACGUCAAGGUGAUUGACGAUGCUAAUCCCAAACGCAUUGUGGAUCGGG
...-........(((..(((.........))).........((((((((..(((((.((....)).....((((((.....)))))).......)))))..))))))))...))).. ( -32.20)
>consensus
GAA_AAACAAGAACAAGGCCAAAAUCAAGUCCAAGAAGCAAACAAUGCGCCUGGGCCGAAAGCUCAUACACGUCAAAGUCAUCGACGAUAAGCAACCAAAGCGCAUUGUGGACCGGA
.........................................(((((((((...((((((..(((............)))..)))..........)))...)))))))))........ (-16.38 = -15.38 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,042,923 – 7,043,040
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 76.37
Mean single sequence MFE -32.12
Consensus MFE -15.86
Energy contribution -16.42
Covariance contribution 0.56
Combinations/Pair 1.27
Mean z-score -2.12
Structure conservation index 0.49
SVM decision value 0.83
SVM RNA-class probability 0.862128
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7042923 117 - 27905053
UGCGGUCCACAAUACGCUUUGGCUGCUUAUCAUCGAUGACUUUUACAUGGAUCAGCUUUCGGCCCACGCGCAUUGUGUGCUUCUUGGACUUUAUUUUGGCCGUGUUCUUGCUUCUUC
.((((((((((((.(((...(((((......(((.(((.......))).))).......)))))...))).))))))..((....))..........)))))).............. ( -28.52)
>DroPse_CAF1 439 116 - 1
CCCGAUCCACAAUGCGUUUGGGAUUAGCAUCGUCAAUCACCUUGACGUGUAUGAGUUUUCGUCCCAGACGCAUUGUUUGCUUAUUGGCCUUCAUUUUGCCCUUCGUUUUGUUA-GAC
..(((...((((((((((((((((..(((.((((((.....)))))))))..(......))))))))))))))))).........(((.........)))..)))........-... ( -35.90)
>DroEre_CAF1 596 117 - 1
UUCGGUCCACAAUACGCUUUGGUUGCUUAUCAUCGAUGACUUUCACAUGGAUUAGCUUUCGGCCCAUGCGCAUUGUGUGCUUCUUGGAUUUGAUUUUGGCCGAGUUAUUGAUUCUUC
(((((((((((((.(((...(((((......(((.(((.......))).))).......)))))...))).))))))....((........))....)))))))............. ( -27.42)
>DroYak_CAF1 602 117 - 1
UUCGGUCCACAAUGCGCUUUGGCUGCUUAUCAUCGAUGACUUUCACAUGAAUAAGCUUUCGGCCCAUGCGCAUUGUGUGCUUCUUGGAUUUGAUUUUGGCCGAGUUCUUGAUUCUUC
...((..((((((((((...(((((((((((((.(.((.....)))))).))))))....))))...))))))))))..))((..(((((((........)))))))..))...... ( -39.40)
>DroAna_CAF1 374 111 - 1
UCCGGUCCACAAUGCGCUUUGGUUGUUUGUCGUCAAUGACUUUAACGUGAAUCAGCUUUCGGCCCAGGCGCAUCGUUUUUUUAUUGGACUUAUUCUUCACCUUCAUCUUGC------
...(((((((.((((((((.(((((((.((((....))))...)))..(((......))))))).)))))))).)).........))))).....................------ ( -26.10)
>DroPer_CAF1 613 116 - 1
CCCGAUCCACAAUGCGUUUGGGAUUAGCAUCGUCAAUCACCUUGACGUGUAUGAGUUUUCGUCCCAGGCGCAUUGUUUGCUUAUUGGCCUUCAUUUUGCCCUUCGUUUUGUUU-GAC
..(((...((((((((((((((((..(((.((((((.....)))))))))..(......))))))))))))))))).........(((.........)))..)))........-... ( -35.40)
>consensus
UCCGGUCCACAAUGCGCUUUGGAUGCUUAUCAUCAAUGACUUUCACAUGAAUCAGCUUUCGGCCCAGGCGCAUUGUGUGCUUAUUGGACUUCAUUUUGGCCGUCUUCUUGAUU_UUC
...((((((((((((((...(((((..........(((.......)))...........)))))...))))))))).........)))))........................... (-15.86 = -16.42 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,042,963 – 7,043,074
Length 111
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.62
Mean single sequence MFE -37.36
Consensus MFE -19.77
Energy contribution -20.30
Covariance contribution 0.53
Combinations/Pair 1.44
Mean z-score -1.70
Structure conservation index 0.53
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7042963 111 - 27905053
UGCUCGCAGAUGCAGGGCUUGGCGCUGGGUCCAUUGCGGUCCACAAUACGCUUUGGCUG---CUUAUCAUCGAUGACUUUUACAUGGAUCAGCUUUCGGCCCACGCGCAUUGUG
.((((((....)).))))...((((((((((((..(((..........)))..))((((---......(((.(((.......))).)))))))....)))))).))))...... ( -36.90)
>DroPse_CAF1 478 111 - 1
UGCUCACAGAUACAGGGCUUGGCGAUUUGGCUGUCCCGAUCCACAAUGCGUUUGGGAUU---AGCAUCGUCAAUCACCUUGACGUGUAUGAGUUUUCGUCCCAGACGCAUUGUU
........(((...(((..((((......)))).))).))).((((((((((((((((.---.(((.((((((.....)))))))))..(......))))))))))))))))). ( -41.80)
>DroWil_CAF1 343 114 - 1
UGCUCACAUAUGCAGGGUUUGGCCGUUUGACCAUCCCGAUCCAUAAUCCGUUUGGGUUGCUCCUUAUCAUCAAUUACUUUCACAUGGAUGAGUUUGCGUCCCAGACGCAUGGUU
(((........)))(((..(((........))).)))...((((....((((((((.(((..((((((..................))))))...))).)))))))).)))).. ( -32.27)
>DroYak_CAF1 642 111 - 1
UGCUCGCAGAUGCAGGGCUUGGCACUGGGUCCAUUUCGGUCCACAAUGCGCUUUGGCUG---CUUAUCAUCGAUGACUUUCACAUGAAUAAGCUUUCGGCCCAUGCGCAUUGUG
.((((((....)).))))..((.((((((.....))))))))(((((((((...(((((---((((((((.(.((.....)))))).))))))....))))...))))))))). ( -40.60)
>DroAna_CAF1 408 111 - 1
UGUUCGCAGAUGCAGGGCUUCGCUGUGGUGCUAUUCCGGUCCACAAUGCGCUUUGGUUG---UUUGUCGUCAAUGACUUUAACGUGAAUCAGCUUUCGGCCCAGGCGCAUCGUU
.((((((....)).)))).....(((((.(((.....))))))))((((((((.(((((---((.((((....))))...)))..(((......))))))).)))))))).... ( -31.30)
>DroPer_CAF1 652 111 - 1
UGCUCACAGAUACAGGGCUUGGCGAUUUGGCUGUCCCGAUCCACAAUGCGUUUGGGAUU---AGCAUCGUCAAUCACCUUGACGUGUAUGAGUUUUCGUCCCAGGCGCAUUGUU
........(((...(((..((((......)))).))).))).((((((((((((((((.---.(((.((((((.....)))))))))..(......))))))))))))))))). ( -41.30)
>consensus
UGCUCACAGAUGCAGGGCUUGGCGAUGGGGCCAUCCCGAUCCACAAUGCGCUUGGGAUG___CUUAUCAUCAAUGACUUUCACAUGAAUGAGCUUUCGGCCCAGGCGCAUUGUU
..............((((((((........)))....)))))(((((((((((.(((((...((((((((.............))).)))))....))))).))))))))))). (-19.77 = -20.30 +   0.53)

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 10:40:18 2006