Locus 581

Sequence ID 3L_DroMel_CAF1
Location 1,676,706 – 1,676,835
Length 129
Max. P 0.954157
window888 window889 window890

overview

Window 8

Location 1,676,706 – 1,676,821
Length 115
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 82.12
Mean single sequence MFE -32.13
Consensus MFE -21.50
Energy contribution -22.17
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.67
SVM decision value 0.03
SVM RNA-class probability 0.548930
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1676706 115 - 23771897
CAGUUGCUGCUGGGCCACGAAAUUGUUUU-GCGCAGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAGCCUCCCACUUCCACUUCUCGAUUUCA
((.(((((((((.((.(((....)))...-)).))))))))).)).(..(((((((.((.(((((.((.....(((((........)))))..))))))).)).)).)))))..). ( -34.40)
>DroPse_CAF1 43674 94 - 1
GAGUU-----UGGGGCAAGAAAUUGGUCG-GCGCUGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAGCCUCCCACAA----------------
.....-----((((((((....)))...(-((((....))..(((((..(((((....(((((((...))))))))))))..)))))..))))))))...---------------- ( -30.00)
>DroWil_CAF1 49334 95 - 1
AGGCU-----AAAGGAAAGAAAUGGUUUUGGCGCAGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAGCCUCCCACUA----------------
(((((-----....((((((.............(((((((......))))))).....(((((((...)))))))....))))))...))))).......---------------- ( -29.20)
>DroMoj_CAF1 46063 97 - 1
--GCAGCUGCCAGGGAACGAGAUUGUUUU-GCGCAGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAACCUCCCACAA----------------
--((.(((((((..(((((....))))))-).))))).))..(((((..(((((....(((((((...))))))))))))..))))).............---------------- ( -29.00)
>DroAna_CAF1 37511 99 - 1
AGGUUGCUGCCGGGGCAAGAAAUGGUUUU-GCGCAGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAGCCUCCCACAA----------------
.((..(((((((((((.(....).)))))-).)))))(((..(((((..(((((....(((((((...))))))))))))..)))))..)))..))....---------------- ( -36.70)
>DroPer_CAF1 43813 94 - 1
GAGUU-----UGGGCCAAGAAAUUGGUCG-GCGCUGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAGCCUCCCACAA----------------
.(((.-----(.((((((....)))))).-).)))..(((..(((((..(((((....(((((((...))))))))))))..)))))..)))........---------------- ( -33.50)
>consensus
AAGUU_____UGGGGCAAGAAAUUGUUUU_GCGCAGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUCAAUUUUUCAUGAGCCUCCCACAA________________
...........(((................((...))(((..(((((..(((((....(((((((...))))))))))))..)))))..))).))).................... (-21.50 = -22.17 +   0.67)

alignment

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secondary structure

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Window 9

Location 1,676,745 – 1,676,835
Length 90
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 72.79
Mean single sequence MFE -28.62
Consensus MFE -16.30
Energy contribution -16.63
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.57
SVM decision value 1.02
SVM RNA-class probability 0.901040
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1676745 90 + 23771897
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCC---GCUGCGCAAAACAAUUUCGUGGCCCAGCAGCAACUGCAGUC---------------------UCAUUUUGA-
..(((((((...)))))))..........(((((..(((.---((((.((...((......)).)).)))).)))..)).))).---------------------.........- ( -24.60)
>DroVir_CAF1 48472 101 + 1
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCCGCCGCUGAGCAAAACAAUUUUGUUUCUUGGCAGCUGC--CAGU--------UUGAG-CCUCG---CCCGUUUUUU
..(((((((...)))))))..........(((((.((((.((.((..((..(((((....)))))))..)).)).).--))).--------.))))-)....---.......... ( -30.90)
>DroGri_CAF1 45427 110 + 1
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCC---GCUGCGCAAAACAAUUUCGUUCCUUGGCAGCUGC--CACUUUUGCAGCUUGGAGUCUCCUCUGCUGCUAAUG
..(((((((...)))))))..................((.---(((((.((((((......)))..)))))))).))--.......(((((..((.....))...)))))..... ( -32.80)
>DroYak_CAF1 39448 90 + 1
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCC---GCUGCGCAAAACAAUUUCGUGCCCCAGCAGCAGCUUCAGCC---------------------UCAUUUUCA-
..(((((((...)))))))..........(((...((((.---((((.(((...........)))..)))).))))....))).---------------------.........- ( -23.60)
>DroMoj_CAF1 46086 105 + 1
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCC---GCUGCGCAAAACAAUCUCGUUCCCUGGCAGCUGC--CAGU-UGGCAGUUUGGA-CUUUG---GGUGCUAUUU
..(((((((...)))))))..........(((((....((---(((((.((((((......)))..(((((....))--))))-)))))))..)).-...))---)))....... ( -32.10)
>DroAna_CAF1 37534 89 + 1
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCC---GCUGCGCAAAACCAUUUCUUGCCCCGGCAGCAACCUGGGCU---------------------UCGGAUUC--
..(((((((...)))))))....((...((((((.(((((---(..(.((((.........))))).)))))).....))))))---------------------...))...-- ( -27.70)
>consensus
GAGCAAGUGCCGCACUUGCAAUUUCAACAGCUCAUCUGCC___GCUGCGCAAAACAAUUUCGUGCCCCGGCAGCAGC__CAGU______________________UCAGUUUCU_
..(((((((...)))))))..........((......))....(((((.....((......))......)))))......................................... (-16.30 = -16.63 +   0.33)

alignment

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secondary structure

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Window 0

Location 1,676,745 – 1,676,835
Length 90
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 72.79
Mean single sequence MFE -34.03
Consensus MFE -18.35
Energy contribution -17.88
Covariance contribution -0.47
Combinations/Pair 1.18
Mean z-score -2.01
Structure conservation index 0.54
SVM decision value 1.44
SVM RNA-class probability 0.954157
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1676745 90 - 23771897
-UCAAAAUGA---------------------GACUGCAGUUGCUGCUGGGCCACGAAAUUGUUUUGCGCAGC---GGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
-((((....(---------------------(.((.((.(((((((((.((.(((....)))...)).))))---))))).)))))).))))....(((((((...))))))).. ( -30.40)
>DroVir_CAF1 48472 101 - 1
AAAAAACGGG---CGAGG-CUCAA--------ACUG--GCAGCUGCCAAGAAACAAAAUUGUUUUGCUCAGCGGCGGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
.......(((---(((((-((...--------(((.--(((((((....((((((....))))))...))))((((((......)))))).....))).)))..))).))))))) ( -34.90)
>DroGri_CAF1 45427 110 - 1
CAUUAGCAGCAGAGGAGACUCCAAGCUGCAAAAGUG--GCAGCUGCCAAGGAACGAAAUUGUUUUGCGCAGC---GGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
..((((((((.(((....)))...(((((.....((--((....)))).((((((....))))))..)))))---.........))))))))....(((((((...))))))).. ( -41.80)
>DroYak_CAF1 39448 90 - 1
-UGAAAAUGA---------------------GGCUGAAGCUGCUGCUGGGGCACGAAAUUGUUUUGCGCAGC---GGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
-.........---------------------((((.(.(((((((((..((((......))))..).)))))---)))...).)))).........(((((((...))))))).. ( -31.10)
>DroMoj_CAF1 46086 105 - 1
AAAUAGCACC---CAAAG-UCCAAACUGCCA-ACUG--GCAGCUGCCAGGGAACGAGAUUGUUUUGCGCAGC---GGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
.((((((...---.....-......(((((.-...)--))))(((((..((((((....))))))((...))---)))))....))))))......(((((((...))))))).. ( -33.50)
>DroAna_CAF1 37534 89 - 1
--GAAUCCGA---------------------AGCCCAGGUUGCUGCCGGGGCAAGAAAUGGUUUUGCGCAGC---GGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
--...((...---------------------(((.((.((((((((((((((.(....).)))))).)))))---)))...)).)))...))....(((((((...))))))).. ( -32.50)
>consensus
_AAAAACAGA______________________ACUG__GCAGCUGCCAGGGAACGAAAUUGUUUUGCGCAGC___GGCAGAUGAGCUGUUGAAAUUGCAAGUGCGGCACUUGCUC
.........................................((((((((((..........))))).)))))...(((((.....)))))......(((((((...))))))).. (-18.35 = -17.88 +  -0.47)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:53 2006