Locus 6868

Sequence ID 3L_DroMel_CAF1
Location 18,456,098 – 18,456,234
Length 136
Max. P 0.806144
window11138 window11139 window11140

overview

Window 8

Location 18,456,098 – 18,456,199
Length 101
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 80.61
Mean single sequence MFE -34.15
Consensus MFE -17.58
Energy contribution -18.90
Covariance contribution 1.32
Combinations/Pair 1.17
Mean z-score -2.60
Structure conservation index 0.51
SVM decision value 0.63
SVM RNA-class probability 0.806144
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18456098 101 + 23771897
ACAGUGAGUGUGUCCU-----GUUGUCUGGUCUUGUUCGCUCGACAGCCAGCUUCUGACCGGGACAAAAAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
.(((((((..((((((-----.((((((((((..(((.(((....))).)))....)))).))))))...)))(((((((....))))))))))..))..))))). ( -32.50)
>DroSec_CAF1 96683 101 + 1
ACAGUGAGCGUGUCCU-----GUUGUCUGGUCUCGUUCACUGGACAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
.(((((.((.((((((-----(.((((..((.......))..))))(((((...))))))))))))((((.(.(((((((....))))))).).))))))))))). ( -41.00)
>DroSim_CAF1 87551 101 + 1
ACAGUGAGCGUGUCCU-----GUUGUCUGGUCUCGUUCACUGGCCAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
.(((((.((.((((((-----(.....(((((.........)))))(((((...))))))))))))((((.(.(((((((....))))))).).))))))))))). ( -38.60)
>DroEre_CAF1 94840 88 + 1
GCAGUGACAGUGUCCUUGC-----GCCUGGUCUUGCUCGCUCGACAGCCAG-------------CAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
.(((((.(((..(......-----((((.((.(((((.(((....))).))-------------))))).))))((((((....))))))...)..))).))))). ( -25.60)
>DroYak_CAF1 97841 104 + 1
--AAUGACAGUGGCCGUUCCCGUUGUCUGCUCUUGUUCGCUCGACAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
--.....(((((((.((.((((.((((.((........))..))))(((((...))))))))))).((((.(.(((((((....))))))).).))))))))))). ( -38.60)
>DroAna_CAF1 92942 101 + 1
UCGAUAUCCGAGUCCC-----GUUGGCUGUUCCCAUUCGUUUGUCAGUUAGCUCCUGGCUGGGAUAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
(((((((((.((((..-----((((((((....((......)).))))))))....)))).)))))((((.(.(((((((....))))))).).))))....)))) ( -28.60)
>consensus
ACAGUGACCGUGUCCU_____GUUGUCUGGUCUCGUUCGCUCGACAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGA
.(((((....((((((.....((((.(((...............))).))))........))))))((((.(.(((((((....))))))).).))))..))))). (-17.58 = -18.90 +   1.32)

alignment

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secondary structure

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Window 9

Location 18,456,098 – 18,456,199
Length 101
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 80.61
Mean single sequence MFE -29.73
Consensus MFE -18.72
Energy contribution -19.62
Covariance contribution 0.89
Combinations/Pair 1.31
Mean z-score -1.56
Structure conservation index 0.63
SVM decision value 0.09
SVM RNA-class probability 0.577607
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18456098 101 - 23771897
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUUUUUGUCCCGGUCAGAAGCUGGCUGUCGAGCGAACAAGACCAGACAAC-----AGGACACACUCACUGU
...(((....)))..(((((((....)))))))(((...(((((..((((....(((.(....).)))......)))).))))).-----)))............. ( -24.30)
>DroSec_CAF1 96683 101 - 1
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUGUUUGUCCCGGCCAGAAGCUGGCUGUCCAGUGAACGAGACCAGACAAC-----AGGACACGCUCACUGU
.....(((((((.(.(((((((....))))))).).)).))))).(((((((...)))))))..((((((.((.(.((.......-----.)).).)).)))))). ( -32.20)
>DroSim_CAF1 87551 101 - 1
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUGUUUGUCCCGGCCAGAAGCUGGCUGGCCAGUGAACGAGACCAGACAAC-----AGGACACGCUCACUGU
.....(((((((.(.(((((((....))))))).).)).)))))((((((((...)))))))).((((((.((.(.((.......-----.)).).)).)))))). ( -35.30)
>DroEre_CAF1 94840 88 - 1
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUGUUUG-------------CUGGCUGUCGAGCGAGCAAGACCAGGC-----GCAAGGACACUGUCACUGC
.((.(((((......(((((((....)))))))(((((((((-------------((.(((....))).)))))........-----))))))....))))).)). ( -27.40)
>DroYak_CAF1 97841 104 - 1
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUGUUUGUCCCGGCCAGAAGCUGGCUGUCGAGCGAACAAGAGCAGACAACGGGAACGGCCACUGUCAUU--
.((.((((((((.(.(((((((....))))))).).))))..((((((((((...)))))((((..((........)).)))).)))))...)))).)).....-- ( -36.90)
>DroAna_CAF1 92942 101 - 1
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUGUUUAUCCCAGCCAGGAGCUAACUGACAAACGAAUGGGAACAGCCAAC-----GGGACUCGGAUAUCGA
....((((((((.(.(((((((....))))))).).))))..(((((..(((.......))).(....)..)))))...))))..-----................ ( -22.30)
>consensus
UCAAUGGCAACAUGUUUAGCAAUUGAUUGCUAACCUUGUUUGUCCCGGCCAGAAGCUGGCUGUCGAGCGAACAAGACCAGACAAC_____AGGACACGCUCACUGU
...(((....)))..(((((((....))))))).(((((((((..(((((((...)))))))....)))))))))............................... (-18.72 = -19.62 +   0.89)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,456,133 – 18,456,234
Length 101
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 86.49
Mean single sequence MFE -29.33
Consensus MFE -21.38
Energy contribution -22.85
Covariance contribution 1.47
Combinations/Pair 1.08
Mean z-score -2.61
Structure conservation index 0.73
SVM decision value -0.03
SVM RNA-class probability 0.517252
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18456133 101 + 23771897
UCGACAGCCAGCUUCUGACCGGGACAAAAAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCAAGCCU-----AACAAAAGUCCGACCC
....(((.......)))....((((.....((((((((((....))))))....((.(((((((......))))))).)).))))-----.......))))..... ( -24.00)
>DroSec_CAF1 96718 101 + 1
UGGACAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCAAGCCU-----AACAAAAGUCCGACCC
.((((.(((((...))))).(((.(.((((.(.(((((((....))))))).).))))((((((......)))))).....))))-----.......))))..... ( -33.00)
>DroSim_CAF1 87586 101 + 1
UGGCCAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCAAGCCU-----AACAAAAGUCCGACCC
.((((((.......)))))).((((.((((.(.(((((((....))))))).).))))((((((......)))))).........-----.......))))..... ( -34.50)
>DroEre_CAF1 94875 88 + 1
UCGACAGCCAG-------------CAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCAUGCCU-----AACAAAAGUCCGACCC
..(((.(....-------------).....((((((((((....))))))).((((.(((((((......))))))).)))))))-----.......)))...... ( -23.40)
>DroYak_CAF1 97879 101 + 1
UCGACAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCAUGCCU-----AACAAAAGUCCGACCC
....(.(((((...))))).)((((........(((((((....))))))).((((.(((((((......))))))).))))...-----.......))))..... ( -33.10)
>DroAna_CAF1 92977 104 + 1
UUGUCAGUUAGCUCCUGGCUGGGAUAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCACCCACUACUGCACCAUACUCCUU--C
.((.((((.(((.....)))(((...((((.(.(((((((....))))))).).))))((((((......))))))....)))...))))))...........--. ( -28.00)
>consensus
UCGACAGCCAGCUUCUGGCCGGGACAAACAAGGUUAGCAAUCAAUUGCUAAACAUGUUGCCAUUGACGAUGAUGGCACCAAGCCU_____AACAAAAGUCCGACCC
......(((((...)))))..((((......(.(((((((....))))))).).((.(((((((......))))))).)).................))))..... (-21.38 = -22.85 +   1.47)

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 12:31:45 2006