Locus 3376

Sequence ID 3L_DroMel_CAF1
Location 9,874,558 – 9,874,694
Length 136
Max. P 0.993932
window5276 window5277 window5278 window5279

overview

Window 6

Location 9,874,558 – 9,874,670
Length 112
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 75.45
Mean single sequence MFE -31.15
Consensus MFE -16.59
Energy contribution -16.73
Covariance contribution 0.14
Combinations/Pair 1.24
Mean z-score -2.38
Structure conservation index 0.53
SVM decision value 1.79
SVM RNA-class probability 0.977468
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9874558 112 + 23771897
GAGAAGAACGCCCUUCUGGAGCUGGAAGUGGAUGAAAAGGGAUUGCUGCAGGAAAAACUACAGCGAUUAAUGGAUGAGACGAGAGGUGGAUGCAUCUAUACCAGAUGUCCAG
.(((((......)))))(((.((((..(((((((......((((((((.((......)).))))))))...........(....).......))))))).))))...))).. ( -32.10)
>DroVir_CAF1 32902 102 + 1
GAGAAAAAUGCACUUCUCGAGAUGGAGGUGGACGAAAAGGAAAUGCUGCAGGAGAAGCUGCAGCGGCUAAUGGACGAGACCCGCGGUGAGUUAC---ACAU--GCA-----A
..........(((((((......)))))))........((...((((((((......)))))))).))...((.......))((((((.....)---)).)--)).-----. ( -27.10)
>DroGri_CAF1 34498 104 + 1
GAAAAGAAUGCGCUCCUUGAGAUGGAGGUGGACGAGAAGGAGAUGCUGCAAGAGAAGCUGCAGCGGCUAAUGGACGAGACCCGCGGUGCGUUUUGUGAUAU--GA------G
....((((((((((((.......))).((((.((...(..((.(((((((........))))))).))..)...))....)))).))))))))).......--..------. ( -28.50)
>DroEre_CAF1 37686 103 + 1
GAAAAGAACGCCCUUCUAGAGCUGGAAGUGGAUGAAAAGGGAUUGCUGCAGGAAAAACUGCAGCGGUUGAUGGAUGAGACGAGAGGUGGGUGCUUCUAGGU---------AG
........((((((((((....)))))).)).))......(((((((((((......)))))))))))..........((.((((((....))))))..))---------.. ( -32.00)
>DroYak_CAF1 36620 102 + 1
GAGAAGAACGCCCUUCUAGAGCUGGAAGUGGAUGAAAAGGGAUUGCUGCAGGAAAAACUGCAGCGGUUGAUGGAUGAGACGAGAGGUGGGUGCUUCUAGGU---------G-
.(((((..((((((((((....))))))............(((((((((((......)))))))))))................))))....)))))....---------.- ( -33.30)
>DroAna_CAF1 34602 104 + 1
GAGAAGAACGCUCUUCUCGAGCUGGAGGUAGACGAAAAGGGUGUGUUGCAGGAGAAGCUGCAGCGGUUGAUGGAUGAGACGAGAGGUGCGU----CCAAAUCUGAU----AG
.......((((((((.(((..(((....))).))).))))))))(((((((......)))))))((((..((((((...(....)...)))----)))))))....----.. ( -33.90)
>consensus
GAGAAGAACGCCCUUCUAGAGCUGGAAGUGGACGAAAAGGGAUUGCUGCAGGAAAAACUGCAGCGGUUAAUGGAUGAGACGAGAGGUGGGUGCUUCUAGAU__GA_____AG
........(((((((((......)))))...............((((((((......))))))))...................))))........................ (-16.59 = -16.73 +   0.14)

alignment

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secondary structure

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Window 7

Location 9,874,558 – 9,874,670
Length 112
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 75.45
Mean single sequence MFE -23.09
Consensus MFE -13.71
Energy contribution -13.10
Covariance contribution -0.61
Combinations/Pair 1.42
Mean z-score -2.73
Structure conservation index 0.59
SVM decision value 2.44
SVM RNA-class probability 0.993932
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9874558 112 - 23771897
CUGGACAUCUGGUAUAGAUGCAUCCACCUCUCGUCUCAUCCAUUAAUCGCUGUAGUUUUUCCUGCAGCAAUCCCUUUUCAUCCACUUCCAGCUCCAGAAGGGCGUUCUUCUC
(((((....(((...(((((...........)))))...)))......(((((((......)))))))..................)))))....((((((....)))))). ( -24.80)
>DroVir_CAF1 32902 102 - 1
U-----UGC--AUGU---GUAACUCACCGCGGGUCUCGUCCAUUAGCCGCUGCAGCUUCUCCUGCAGCAUUUCCUUUUCGUCCACCUCCAUCUCGAGAAGUGCAUUUUUCUC
.-----(((--(.((---(.....))).((.((......))....)).(((((((......))))))).....(((((((.............)))))))))))........ ( -24.42)
>DroGri_CAF1 34498 104 - 1
C------UC--AUAUCACAAAACGCACCGCGGGUCUCGUCCAUUAGCCGCUGCAGCUUCUCUUGCAGCAUCUCCUUCUCGUCCACCUCCAUCUCAAGGAGCGCAUUCUUUUC
.------..--.................(((((...((......((..(((((((......)))))))..))......)).))..((((.......)))))))......... ( -21.30)
>DroEre_CAF1 37686 103 - 1
CU---------ACCUAGAAGCACCCACCUCUCGUCUCAUCCAUCAACCGCUGCAGUUUUUCCUGCAGCAAUCCCUUUUCAUCCACUUCCAGCUCUAGAAGGGCGUUCUUUUC
..---------....(((((.((((.......................(((((((......)))))))................((((........)))))).)).))))). ( -21.10)
>DroYak_CAF1 36620 102 - 1
-C---------ACCUAGAAGCACCCACCUCUCGUCUCAUCCAUCAACCGCUGCAGUUUUUCCUGCAGCAAUCCCUUUUCAUCCACUUCCAGCUCUAGAAGGGCGUUCUUCUC
-.---------....(((((.((((.......................(((((((......)))))))................((((........)))))).)).))))). ( -23.70)
>DroAna_CAF1 34602 104 - 1
CU----AUCAGAUUUGG----ACGCACCUCUCGUCUCAUCCAUCAACCGCUGCAGCUUCUCCUGCAACACACCCUUUUCGUCUACCUCCAGCUCGAGAAGAGCGUUCUUCUC
..----...(((...((----((((.......................(.(((((......))))).).....(((((((.((......))..))))))).)))))).))). ( -23.20)
>consensus
CU_____UC__AUAUAGAAGCACCCACCUCUCGUCUCAUCCAUCAACCGCUGCAGCUUCUCCUGCAGCAAUCCCUUUUCAUCCACCUCCAGCUCGAGAAGGGCGUUCUUCUC
................................................(((((((......)))))))...........................(((((......))))). (-13.71 = -13.10 +  -0.61)

alignment

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secondary structure

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Window 8

Location 9,874,598 – 9,874,694
Length 96
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 73.21
Mean single sequence MFE -23.62
Consensus MFE -9.88
Energy contribution -10.13
Covariance contribution 0.25
Combinations/Pair 1.32
Mean z-score -1.87
Structure conservation index 0.42
SVM decision value 0.16
SVM RNA-class probability 0.611328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9874598 96 + 23771897
GAUUGCUGCAGGAAAAACUACAGCGAUUAAUGGAUGAGACGAGAGGUGGAUGCAUCUAUACCAGAUGUCCAGCACAGACU--U--UAAAACUAAUUCAUC
((((((((.((......)).))))))))....((((((.(....).(((..((((((.....))))))))).........--.--.........)))))) ( -23.40)
>DroSec_CAF1 35559 95 + 1
GUUUGCUGCAGGAAAAACUACAGCGAUUAAUGGAUGAGACGAGAGGUGGAUGAUUCAAGACCAGACGUUCAGUACAAACU-----CAAAACUAAUUUAUC
..((((((.((......)).))))))........((((.(....).((((((..((.......)))))))).......))-----))............. ( -16.10)
>DroSim_CAF1 37462 95 + 1
GUUUGCUGCAGGAGAAACUACAGCGAUUAAUGGAUGAGACGAGAGGUGGAUGAUUCAAGACCAGACGUUCAGUACAAACU-----CAAAACUAAUUCAUC
..((((((.((......)).))))))...((((((.((..(((.(((.((....))...)))..((.....)).....))-----)....)).)))))). ( -16.90)
>DroEre_CAF1 37726 89 + 1
GAUUGCUGCAGGAAAAACUGCAGCGGUUGAUGGAUGAGACGAGAGGUGGGUGCUUCUAGGU---------AGUACAGACUAAUUCA--AACUAAUUCAUC
(((((((((((......)))))))))))(((((((.((.(.((((((....)))))).).(---------(((....)))).....--..)).))))))) ( -30.50)
>DroYak_CAF1 36660 87 + 1
GAUUGCUGCAGGAAAAACUGCAGCGGUUGAUGGAUGAGACGAGAGGUGGGUGCUUCUAGGU---------G----AAACCAAAUCAAAAACUAAUUCAUU
(((((((((((......)))))))))))(((((((.((...((((((....)))))).((.---------.----...))..........)).))))))) ( -29.40)
>DroAna_CAF1 34642 82 + 1
GUGUGUUGCAGGAGAAGCUGCAGCGGUUGAUGGAUGAGACGAGAGGUGCGU----CCAAAUCUGAU----AGUCUAAACU-----AUUA----AGUC-UU
....(((((((......)))))))((((..((((((...(....)...)))----)))))))((((----(((....)))-----))))----....-.. ( -25.40)
>consensus
GAUUGCUGCAGGAAAAACUACAGCGAUUAAUGGAUGAGACGAGAGGUGGAUGCUUCUAGACCAGA_____AGUACAAACU_____AAAAACUAAUUCAUC
..((((((.((......)).))))))......((((((.(....).((((....))))....................................)))))) ( -9.88 = -10.13 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,874,598 – 9,874,694
Length 96
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 73.21
Mean single sequence MFE -19.00
Consensus MFE -10.92
Energy contribution -10.83
Covariance contribution -0.08
Combinations/Pair 1.14
Mean z-score -1.67
Structure conservation index 0.57
SVM decision value 0.82
SVM RNA-class probability 0.859072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9874598 96 - 23771897
GAUGAAUUAGUUUUA--A--AGUCUGUGCUGGACAUCUGGUAUAGAUGCAUCCACCUCUCGUCUCAUCCAUUAAUCGCUGUAGUUUUUCCUGCAGCAAUC
(((((....((....--.--.((((((((..(....)..))))))))......))...))))).............(((((((......))))))).... ( -27.90)
>DroSec_CAF1 35559 95 - 1
GAUAAAUUAGUUUUG-----AGUUUGUACUGAACGUCUGGUCUUGAAUCAUCCACCUCUCGUCUCAUCCAUUAAUCGCUGUAGUUUUUCCUGCAGCAAAC
.....((((((..((-----((..........(((...(((...((....)).)))...)))))))...)))))).(((((((......))))))).... ( -17.40)
>DroSim_CAF1 37462 95 - 1
GAUGAAUUAGUUUUG-----AGUUUGUACUGAACGUCUGGUCUUGAAUCAUCCACCUCUCGUCUCAUCCAUUAAUCGCUGUAGUUUCUCCUGCAGCAAAC
(((((.(((((....-----.......)))))(((...(((...((....)).)))...))).)))))........(((((((......))))))).... ( -19.90)
>DroEre_CAF1 37726 89 - 1
GAUGAAUUAGUU--UGAAUUAGUCUGUACU---------ACCUAGAAGCACCCACCUCUCGUCUCAUCCAUCAACCGCUGCAGUUUUUCCUGCAGCAAUC
((((...((((.--.((.....))...)))---------)....((..(...........)..))...))))....(((((((......))))))).... ( -18.60)
>DroYak_CAF1 36660 87 - 1
AAUGAAUUAGUUUUUGAUUUGGUUU----C---------ACCUAGAAGCACCCACCUCUCGUCUCAUCCAUCAACCGCUGCAGUUUUUCCUGCAGCAAUC
...(((((((...))))))).((((----(---------.....)))))...........................(((((((......))))))).... ( -17.20)
>DroAna_CAF1 34642 82 - 1
AA-GACU----UAAU-----AGUUUAGACU----AUCAGAUUUGG----ACGCACCUCUCGUCUCAUCCAUCAACCGCUGCAGCUUCUCCUGCAACACAC
.(-((((----....-----))))).....----....(((.(((----(((.......)))).))...)))....(.(((((......))))).).... ( -13.00)
>consensus
GAUGAAUUAGUUUUU_____AGUUUGUACU_____UCUGAUCUAGAAGCACCCACCUCUCGUCUCAUCCAUCAACCGCUGCAGUUUUUCCUGCAGCAAAC
............................................................................(((((((......))))))).... (-10.92 = -10.83 +  -0.08)

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 10:56:38 2006