Locus 6962

Sequence ID X_DroMel_CAF1
Location 17,442,987 – 17,443,132
Length 145
Max. P 0.996591
window11372 window11373 window11374 window11375

overview

Window 2

Location 17,442,987 – 17,443,093
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.67
Mean single sequence MFE -34.83
Consensus MFE -21.11
Energy contribution -22.87
Covariance contribution 1.75
Combinations/Pair 1.04
Mean z-score -2.33
Structure conservation index 0.61
SVM decision value 1.79
SVM RNA-class probability 0.977347
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17442987 106 + 22224390
----AGCACAC---AGCAACUGCAAAGUUAAUCAAAAUGCAAUGUGGUCAAAAGGGCGUGAACA-GGCCAGGUGCACGUCAUAUUCGCACCUUUUGUAAACGACGCCCUUCC------CU
----..((((.---.((((((....))).........)))..)))).....(((((((((.(((-((..((((((...........)))))))))))...).))))))))..------.. ( -27.90)
>DroSec_CAF1 8216 108 + 1
----AGCAUGCAGCAGCAACUGCGAGG-UAAUCG-AAUGCGAUGUGGUCAAAAGGGCGUGACCGUUGGCAGGUGCACGUCAUAUUCGCACCUUUUGCGAACGACGCCCUUUC------CU
----.(((((((((((...))))((..-...)).-..))).))))((...(((((((((...((((.((((((((...........)))))...))).))))))))))))))------). ( -39.50)
>DroEre_CAF1 7827 106 + 1
----AGCAC---------ACUGCAAACUUAAUCAAAAUACGUUGUGGUCAAAAGGGCGUUAACA-GGCCAGGCGCAAGUCAUAUUUGCACCUUUUGCAUAUGACGCCCUUACGACGCUUU
----(((.(---------((.((.................)).)))(((..((((((((((...-.((.(((.((((((...)))))).)))...))...))))))))))..)))))).. ( -33.93)
>DroYak_CAF1 7973 115 + 1
ACACAACAC----CGUCAACUGGGAACUUAAUCAAAAUGCGAUGUGGUCAAAAGGGCGUUAACA-GGCCAGGUGCAAGUCAUAUUUGCACCUUUUGCAAACGACGCCCUUGCGACGCUUU
.((((.(.(----((.....)))((......)).......).))))(((..(((((((((....-.((.((((((((((...))))))))))...))....)))))))))..)))..... ( -38.00)
>consensus
____AGCAC_____AGCAACUGCAAACUUAAUCAAAAUGCGAUGUGGUCAAAAGGGCGUGAACA_GGCCAGGUGCAAGUCAUAUUCGCACCUUUUGCAAACGACGCCCUUAC______CU
..................((((((..................))))))...(((((((((.........((((((((((...)))))))))).........))))))))).......... (-21.11 = -22.87 +   1.75)

alignment

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secondary structure

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Window 3

Location 17,442,987 – 17,443,093
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.67
Mean single sequence MFE -37.78
Consensus MFE -26.24
Energy contribution -27.68
Covariance contribution 1.44
Combinations/Pair 1.24
Mean z-score -2.41
Structure conservation index 0.69
SVM decision value 2.59
SVM RNA-class probability 0.995534
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17442987 106 - 22224390
AG------GGAAGGGCGUCGUUUACAAAAGGUGCGAAUAUGACGUGCACCUGGCC-UGUUCACGCCCUUUUGACCACAUUGCAUUUUGAUUAACUUUGCAGUUGCU---GUGUGCU----
..------((((((((((.(...(((..(((((((.........)))))))....-))).)))))))))))...(((((.(((..(((..........))).))).---)))))..---- ( -33.40)
>DroSec_CAF1 8216 108 - 1
AG------GAAAGGGCGUCGUUCGCAAAAGGUGCGAAUAUGACGUGCACCUGCCAACGGUCACGCCCUUUUGACCACAUCGCAUU-CGAUUA-CCUCGCAGUUGCUGCUGCAUGCU----
..------((((((((((((((((((.....)))))..)))))(((.(((.......)))))))))))))).........((((.-.((...-..))(((((....))))))))).---- ( -39.50)
>DroEre_CAF1 7827 106 - 1
AAAGCGUCGUAAGGGCGUCAUAUGCAAAAGGUGCAAAUAUGACUUGCGCCUGGCC-UGUUAACGCCCUUUUGACCACAACGUAUUUUGAUUAAGUUUGCAGU---------GUGCU----
..(((((((.((((((((.(((.((...((((((((.......)))))))).)).-)))..)))))))).)))).(((..(((..((.....))..)))..)---------)))))---- ( -38.20)
>DroYak_CAF1 7973 115 - 1
AAAGCGUCGCAAGGGCGUCGUUUGCAAAAGGUGCAAAUAUGACUUGCACCUGGCC-UGUUAACGCCCUUUUGACCACAUCGCAUUUUGAUUAAGUUCCCAGUUGACG----GUGUUGUGU
.....((((.((((((((.....((...((((((((.......)))))))).)).-.....)))))))).))))((((.(((...(..(((........)))..)..----))).)))). ( -40.00)
>consensus
AA______GAAAGGGCGUCGUUUGCAAAAGGUGCAAAUAUGACGUGCACCUGGCC_UGUUAACGCCCUUUUGACCACAUCGCAUUUUGAUUAACUUCGCAGUUGCU_____GUGCU____
.....(((((((((((((..........((((((((.......))))))))..........)))))))))))))......((((...........................))))..... (-26.24 = -27.68 +   1.44)

alignment

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secondary structure

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Window 4

Location 17,443,020 – 17,443,132
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -40.58
Consensus MFE -31.13
Energy contribution -33.63
Covariance contribution 2.50
Combinations/Pair 1.00
Mean z-score -3.20
Structure conservation index 0.77
SVM decision value 2.72
SVM RNA-class probability 0.996591
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17443020 112 + 22224390
AAUGUGGUCAAAAGGGCGUGAACA-GGCCAGGUGCACGUCAUAUUCGCACCUUUUGUAAACGACGCCCUUCC------CUUAACAUUCGCCACAAAACCAGAA-GUCAGCUCUGUCAUAA
..((((((.(((((((((((.(((-((..((((((...........)))))))))))...).))))))))..------.......)).))))))....((((.-(....)))))...... ( -30.70)
>DroSec_CAF1 8250 113 + 1
GAUGUGGUCAAAAGGGCGUGACCGUUGGCAGGUGCACGUCAUAUUCGCACCUUUUGCGAACGACGCCCUUUC------CUUACCGUUGGCCACAAAACCAGAA-GGCAUCGCUGUCAUAA
..(((((((((((((((((...((((.((((((((...........)))))...))).))))))))))))..------.......))))))))).........-((((....)))).... ( -42.30)
>DroEre_CAF1 7854 119 + 1
GUUGUGGUCAAAAGGGCGUUAACA-GGCCAGGCGCAAGUCAUAUUUGCACCUUUUGCAUAUGACGCCCUUACGACGCUUUUUGCAUUGGCCACAAAACCAGUAAAGCAUCUCUGUCAUAA
.((((((((((((((((((((...-.((.(((.((((((...)))))).)))...))...)))))))))).....((.....)).))))))))))...(((..........)))...... ( -42.10)
>DroYak_CAF1 8009 119 + 1
GAUGUGGUCAAAAGGGCGUUAACA-GGCCAGGUGCAAGUCAUAUUUGCACCUUUUGCAAACGACGCCCUUGCGACGCUUUUUGCAUUGGCCACAAAACCAGAAGGGCAUCUCUGUCAUAA
..((((((((((((((((((....-.((.((((((((((...))))))))))...))....)))))))))((((......)))).)))))))))..........((((....)))).... ( -47.20)
>consensus
GAUGUGGUCAAAAGGGCGUGAACA_GGCCAGGUGCAAGUCAUAUUCGCACCUUUUGCAAACGACGCCCUUAC______CUUAGCAUUGGCCACAAAACCAGAA_GGCAUCUCUGUCAUAA
..((((((((((((((((((.........((((((((((...)))))))))).........)))))))))...............)))))))))....((((........))))...... (-31.13 = -33.63 +   2.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,443,020 – 17,443,132
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.52
Mean single sequence MFE -39.15
Consensus MFE -31.01
Energy contribution -33.01
Covariance contribution 2.00
Combinations/Pair 1.10
Mean z-score -2.04
Structure conservation index 0.79
SVM decision value 1.08
SVM RNA-class probability 0.911388
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17443020 112 - 22224390
UUAUGACAGAGCUGAC-UUCUGGUUUUGUGGCGAAUGUUAAG------GGAAGGGCGUCGUUUACAAAAGGUGCGAAUAUGACGUGCACCUGGCC-UGUUCACGCCCUUUUGACCACAUU
...(.((((((((...-....)))))))).)..(((((....------((((((((((.(...(((..(((((((.........)))))))....-))).)))))))))))....))))) ( -34.50)
>DroSec_CAF1 8250 113 - 1
UUAUGACAGCGAUGCC-UUCUGGUUUUGUGGCCAACGGUAAG------GAAAGGGCGUCGUUCGCAAAAGGUGCGAAUAUGACGUGCACCUGCCAACGGUCACGCCCUUUUGACCACAUC
...((.(.((((.(((-....))).)))).).))..(((...------((((((((((((((((((.....)))))..)))))(((.(((.......)))))))))))))).)))..... ( -40.50)
>DroEre_CAF1 7854 119 - 1
UUAUGACAGAGAUGCUUUACUGGUUUUGUGGCCAAUGCAAAAAGCGUCGUAAGGGCGUCAUAUGCAAAAGGUGCAAAUAUGACUUGCGCCUGGCC-UGUUAACGCCCUUUUGACCACAAC
......((((((((((((..(((((....)))))......))))))))...(((((((.(((.((...((((((((.......)))))))).)).-)))..)))))))))))........ ( -40.20)
>DroYak_CAF1 8009 119 - 1
UUAUGACAGAGAUGCCCUUCUGGUUUUGUGGCCAAUGCAAAAAGCGUCGCAAGGGCGUCGUUUGCAAAAGGUGCAAAUAUGACUUGCACCUGGCC-UGUUAACGCCCUUUUGACCACAUC
...((((((.(((((((((((((((....)))))((((.....)))).).)))))))))....((...((((((((.......)))))))).)))-)))))................... ( -41.40)
>consensus
UUAUGACAGAGAUGCC_UUCUGGUUUUGUGGCCAAUGCAAAA______GAAAGGGCGUCGUUUGCAAAAGGUGCAAAUAUGACGUGCACCUGGCC_UGUUAACGCCCUUUUGACCACAUC
......(((((......)))))....(((((...............((((((((((((..........((((((((.......))))))))..........))))))))))))))))).. (-31.01 = -33.01 +   2.00)

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 12:26:50 2006