Locus 9107

Sequence ID 3R_DroMel_CAF1
Location 24,307,251 – 24,307,390
Length 139
Max. P 0.970498
window14572 window14573 window14574

overview

Window 2

Location 24,307,251 – 24,307,362
Length 111
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.87
Mean single sequence MFE -33.62
Consensus MFE -19.05
Energy contribution -18.91
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -2.80
Structure conservation index 0.57
SVM decision value 1.66
SVM RNA-class probability 0.970498
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24307251 111 + 27905053
G-AGCACUUGGCACAAGGCGUCCUUGCGAGAACGAGAGGCGCCAAAUGAAAACACGUGACGCCCG-----AGCAAUUGGUGGGCAACAAAGCU-CAAGCUUUGAGUUAUGGCCAA-ACG
.-.....(((((....((((((((((......)))).))))))...........(((((((((((-----..(....).)))))..((((((.-...)))))).)))))))))))-... ( -43.70)
>DroVir_CAF1 110625 99 + 1
A-AGCACUUGGCAUGAG-------------AGCG-AAGAAGCCAAAUGAAAACACGUGACGCGAUGCC--AGCAAUUGGUAAGCAACAAAGCU-UCAGCUUUGAGUUAUGGCCAA--CC
.-.....(((((....(-------------.((.-.....)))...........((((((((..((((--((...)))))).))..((((((.-...)))))).)))))))))))--.. ( -28.90)
>DroPse_CAF1 136238 111 + 1
GAAGCACUUGGCAAAAAG-------GCGAGAGCG-GAGGCGCCAAAUGAAAACACGUGACGCCAUCGCAUCGCAAUUGGUAAGCAACAAAGCUUCAAGCUUUGAGUUAUGGCCAACACG
.......(((((......-------((((..(((-..((((.((..((....))..)).))))..))).)))).............((((((.....)))))).......))))).... ( -35.50)
>DroWil_CAF1 101814 96 + 1
A-AGCACUUGGCAUAA--------------AACGAAAGGCGUCAAAUGAAAACACGUGACGCCAA-----AGCAAUUGGUAAGCAACAAAGCU-UCAGCUUUGAGUUAUGGC-AA-ACG
.-.....(((.(((((--------------.......(((((((..((....))..)))))))..-----................((((((.-...))))))..))))).)-))-... ( -27.90)
>DroAna_CAF1 132743 96 + 1
A-AGCACUUGGCAUAAAGC--------------AAGAGGCGCCAAAUGAAAACACGUGACGCCUC-----GGCAAUUGGUGGGCAACAAAGCU-CCGGCUUUGAGUUAUGGCCA--ACG
.-.....(((((((((..(--------------((((((((.((..((....))..)).))))))-----.......(.(((((......)).-))).).)))..)))).))))--).. ( -30.20)
>DroPer_CAF1 136024 111 + 1
GAAGCACUUGGCAAAAAG-------GCGAGAGCG-GAGGCGCCAAAUGAAAACACGUGACGCCAUCGCAUCGCAAUUGGUAAGCAACAAAGCUUCAAGCUUUGAGUUAUGGCCAACACG
.......(((((......-------((((..(((-..((((.((..((....))..)).))))..))).)))).............((((((.....)))))).......))))).... ( -35.50)
>consensus
A_AGCACUUGGCAUAAAG____________AGCG_GAGGCGCCAAAUGAAAACACGUGACGCCAU_____AGCAAUUGGUAAGCAACAAAGCU_CAAGCUUUGAGUUAUGGCCAA_ACG
...((..(((((............................))))).........((((((((.........)).............((((((.....)))))).))))))))....... (-19.05 = -18.91 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,307,251 – 24,307,362
Length 111
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.87
Mean single sequence MFE -33.01
Consensus MFE -23.21
Energy contribution -23.60
Covariance contribution 0.39
Combinations/Pair 1.10
Mean z-score -2.39
Structure conservation index 0.70
SVM decision value 1.54
SVM RNA-class probability 0.962295
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24307251 111 - 27905053
CGU-UUGGCCAUAACUCAAAGCUUG-AGCUUUGUUGCCCACCAAUUGCU-----CGGGCGUCACGUGUUUUCAUUUGGCGCCUCUCGUUCUCGCAAGGACGCCUUGUGCCAAGUGCU-C
((.-.((((.......((((((...-.))))))..((((..........-----.))))))))..))....((((((((((....((((((....))))))....))))))))))..-. ( -36.40)
>DroVir_CAF1 110625 99 - 1
GG--UUGGCCAUAACUCAAAGCUGA-AGCUUUGUUGCUUACCAAUUGCU--GGCAUCGCGUCACGUGUUUUCAUUUGGCUUCUU-CGCU-------------CUCAUGCCAAGUGCU-U
((--(.(((.......((((((...-.))))))..))).)))....(((--(((.....)))).)).....((((((((.....-....-------------.....))))))))..-. ( -24.94)
>DroPse_CAF1 136238 111 - 1
CGUGUUGGCCAUAACUCAAAGCUUGAAGCUUUGUUGCUUACCAAUUGCGAUGCGAUGGCGUCACGUGUUUUCAUUUGGCGCCUC-CGCUCUCGC-------CUUUUUGCCAAGUGCUUC
.((((((((.......((((((.....)))))).............((((.(((..(((((((.(((....))).)))))))..-)))..))))-------......))))).)))... ( -38.30)
>DroWil_CAF1 101814 96 - 1
CGU-UU-GCCAUAACUCAAAGCUGA-AGCUUUGUUGCUUACCAAUUGCU-----UUGGCGUCACGUGUUUUCAUUUGACGCCUUUCGUU--------------UUAUGCCAAGUGCU-U
(((-((-(.(((((..((((((..(-(((......)))).......)))-----))(((((((.(((....))).)))))))....)..--------------))))).))))))..-. ( -27.40)
>DroAna_CAF1 132743 96 - 1
CGU--UGGCCAUAACUCAAAGCCGG-AGCUUUGUUGCCCACCAAUUGCC-----GAGGCGUCACGUGUUUUCAUUUGGCGCCUCUU--------------GCUUUAUGCCAAGUGCU-U
..(--((((.((((..(((....((-.((......))))..........-----(((((((((.(((....))).)))))))))))--------------)..))))))))).....-. ( -32.70)
>DroPer_CAF1 136024 111 - 1
CGUGUUGGCCAUAACUCAAAGCUUGAAGCUUUGUUGCUUACCAAUUGCGAUGCGAUGGCGUCACGUGUUUUCAUUUGGCGCCUC-CGCUCUCGC-------CUUUUUGCCAAGUGCUUC
.((((((((.......((((((.....)))))).............((((.(((..(((((((.(((....))).)))))))..-)))..))))-------......))))).)))... ( -38.30)
>consensus
CGU_UUGGCCAUAACUCAAAGCUGG_AGCUUUGUUGCUUACCAAUUGCU_____AUGGCGUCACGUGUUUUCAUUUGGCGCCUC_CGCU____________CUUUAUGCCAAGUGCU_C
....(((((.......((((((.....)))))).......................(((((((.(((....))).))))))).........................)))))....... (-23.21 = -23.60 +   0.39)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,307,290 – 24,307,390
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 74.56
Mean single sequence MFE -25.61
Consensus MFE -12.73
Energy contribution -12.40
Covariance contribution -0.33
Combinations/Pair 1.20
Mean z-score -1.81
Structure conservation index 0.50
SVM decision value 0.39
SVM RNA-class probability 0.716261
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24307290 100 + 27905053
GCCAAAUGAAAACACGUGACGCCCG-----AGCAAUUGGUGGGCAACAAAGCU-CAAGCUUUGAGUUAUGGCCAA-ACGCAAUGG------UGCACACAAACAAUGGAGGCAG
(((...........(((((((((((-----..(....).)))))..((((((.-...)))))).))))))((((.-......)))------)................))).. ( -30.10)
>DroGri_CAF1 112206 102 + 1
GCCAAAUGAAAACACGUGACGCGAUACC--AGCAAUUGGUAAGCAACAAAGCU-UCAGUUUUGAAUUAUGGCCAU--AGCAGUAG------CAUGCACAAGCAGCCCCAGAAG
((((................((..((((--((...)))))).))..((((((.-...)))))).....))))...--....(..(------(.(((....)))))..)..... ( -22.20)
>DroWil_CAF1 101839 91 + 1
GUCAAAUGAAAACACGUGACGCCAA-----AGCAAUUGGUAAGCAACAAAGCU-UCAGCUUUGAGUUAUGGC-AA-ACGCAAUGG------AAUACACAAACAAC--------
((((..((....))..))))((((.-----(((..(((.....)))((((((.-...)))))).))).))))-..-.........------..............-------- ( -20.40)
>DroMoj_CAF1 89549 102 + 1
GCCAAAUGAAAACACGUGACGCGAUGCC--AGCAAUUGGUAAGCAACAAAGCU-CCAGCUUUGAAUUAUGACCAA--CUGGGUCG------CAUACACAAGCAGCAGGAGCCC
(((...((.......(((..(((((.((--((...(((((......((((((.-...)))))).......)))))--))))))))------)...)))......)).).)).. ( -26.64)
>DroAna_CAF1 132768 94 + 1
GCCAAAUGAAAACACGUGACGCCUC-----GGCAAUUGGUGGGCAACAAAGCU-CCGGCUUUGAGUUAUGGCCA--ACGCAAUGG------CAUAUACAAACAAACAA-----
((((..........(((((((((.(-----(.(....).)))))..((((((.-...)))))).))))))((..--..))..)))------)................----- ( -27.30)
>DroPer_CAF1 136056 113 + 1
GCCAAAUGAAAACACGUGACGCCAUCGCAUCGCAAUUGGUAAGCAACAAAGCUUCAAGCUUUGAGUUAUGGCCAACACGCAACGGCCGAGGCAUAUACAAACAGAAGAGAAGA
(((............(((((((((..((...))...))))......((((((.....)))))).)))))((((..........))))..)))..................... ( -27.00)
>consensus
GCCAAAUGAAAACACGUGACGCCAU_____AGCAAUUGGUAAGCAACAAAGCU_CCAGCUUUGAGUUAUGGCCAA_ACGCAAUGG______CAUACACAAACAACAGA_G___
...............(((..((.........))...((((......((((((.....)))))).......)))).....................)))............... (-12.73 = -12.40 +  -0.33)

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 13:26:43 2006