Locus 1222

Sequence ID 3R_DroMel_CAF1
Location 3,693,671 – 3,693,806
Length 135
Max. P 0.969377
window1998 window1999 window2000

overview

Window 8

Location 3,693,671 – 3,693,766
Length 95
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 78.69
Mean single sequence MFE -18.57
Consensus MFE -13.40
Energy contribution -13.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.72
SVM decision value 1.64
SVM RNA-class probability 0.969377
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3693671 95 + 27905053
CUGUUUCACAUAUAUAUGUAAUUUAUUGU-----UUUUUGUUUU-GGU----UUUAG----UAUGAUAAAUAAAUGCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
.......((((....))))..........-----..........-(((----...((----(((.........)))))..((((((((.....)))))))))))..... ( -17.70)
>DroPse_CAF1 55200 86 + 1
CUUUAUCAGUUU---------UUUUUUG-------UUUUUUUUUUGGUU---UUUAG----UAUUUUAAAUAAAUGCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
............---------.......-------..........(((.---...((----(((((.....)))))))..((((((((.....)))))))))))..... ( -18.90)
>DroSim_CAF1 53612 91 + 1
CUGUUUCACAUAUAU----AAUUAAUUGU-----UUUUGGUUUU-UGU----UUUAG----UAUGAUAAAUAAAUGCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
...............----..........-----....(((...-...----...((----(((.........)))))..((((((((.....)))))))))))..... ( -16.90)
>DroEre_CAF1 51180 101 + 1
CUGUUUCACAUAUAU----AAUUUAUUGUACUUUUUUUUGUUUUCGGUUUUGUUUAG----UAUGAUAAAUAAAUGCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
...............----.((((((..((((.....(((....)))........))----))..)))))).........((((((((.....))))))))........ ( -20.82)
>DroYak_CAF1 49662 97 + 1
CUGUUUCACAUAUAU----AAUUAAUUGUAUUUUUUU----UUUCGGUUUUGUUUAG----UAUGAUAAAUAAAUGCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
...........((((----((....))))))......----....(((((((((((.----.....))))))))......((((((((.....)))))))))))..... ( -19.20)
>DroAna_CAF1 38513 88 + 1
UUGUUUCAUCACU-----------UUGGU-----UUUUGGUUUU-UUU----UUUAGUACGUAUGUGAAAUAAAUUCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
((((((((.((..-----------.((..-----..((((....-...----.))))..))..)))))))))).......((((((((.....))))))))........ ( -17.90)
>consensus
CUGUUUCACAUAUAU____AAUUUAUUGU_____UUUUUGUUUU_GGU____UUUAG____UAUGAUAAAUAAAUGCUUAGCGACGACAAUUUGUUGUCGCACCUUCUU
................................................................................((((((((.....))))))))........ (-13.40 = -13.40 +   0.00)

alignment

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secondary structure

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Window 9

Location 3,693,671 – 3,693,766
Length 95
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 78.69
Mean single sequence MFE -12.53
Consensus MFE -10.60
Energy contribution -10.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.85
SVM decision value 1.15
SVM RNA-class probability 0.922459
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3693671 95 - 27905053
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUUAUCAUA----CUAAA----ACC-AAAACAAAAA-----ACAAUAAAUUACAUAUAUAUGUGAAACAG
.....((((((((.((.....)).)))))..........((((.....----.))))----)))-..........-----........((((((....))))))..... ( -14.00)
>DroPse_CAF1 55200 86 - 1
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUUAAAAUA----CUAAA---AACCAAAAAAAAAA-------CAAAAAA---------AAACUGAUAAAG
.....((((((((.((.....)).)))))..((.((((.....)))).----))...---.)))..........-------.......---------............ ( -11.50)
>DroSim_CAF1 53612 91 - 1
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUUAUCAUA----CUAAA----ACA-AAAACCAAAA-----ACAAUUAAUU----AUAUAUGUGAAACAG
.....((((((((.((.....)).)))))..........((((.....----.))))----...-...)))....-----..........----............... ( -10.80)
>DroEre_CAF1 51180 101 - 1
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUUAUCAUA----CUAAACAAAACCGAAAACAAAAAAAAGUACAAUAAAUU----AUAUAUGUGAAACAG
.....((((((((((....)))))).))))..((((..((((((..((----((.......................))))..)))))).----....))))....... ( -15.00)
>DroYak_CAF1 49662 97 - 1
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUUAUCAUA----CUAAACAAAACCGAAA----AAAAAAAUACAAUUAAUU----AUAUAUGUGAAACAG
.....((((((((.((.....)).)))))......(((.((((.....----.)))).))))))....----..................----............... ( -10.90)
>DroAna_CAF1 38513 88 - 1
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGAAUUUAUUUCACAUACGUACUAAA----AAA-AAAACCAAAA-----ACCAA-----------AGUGAUGAAACAA
.....((((((((.((.....)).)))))...(((.....)))..............----...-...)))....-----.....-----------.((......)).. ( -13.00)
>consensus
AAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUUAUCAUA____CUAAA____ACC_AAAACAAAAA_____ACAAUAAAUU____AUAUAUGUGAAACAG
.....((((((((((....)))))).))))............................................................................... (-10.60 = -10.60 +  -0.00)

alignment

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secondary structure

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Window 0

Location 3,693,701 – 3,693,806
Length 105
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.85
Mean single sequence MFE -18.35
Consensus MFE -14.55
Energy contribution -14.72
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.79
SVM decision value 0.26
SVM RNA-class probability 0.656113
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3693701 105 - 27905053
GGCUUGCCGACGGUGCAUAAAAAACGAACAACAAAUCAGAAAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUU----A-UCAUA----CUAAA----ACC-AAAACAAAA
.(((((.((((...((((.......((........)).........))))(((((....))))))))).)))))........----.-.....----.....----...-......... ( -18.59)
>DroVir_CAF1 67220 94 - 1
GGCUUGCCAACGGUGCAUAAAAAACGUACAACAAAUCAGAAAGAAGGUGCGACAGCAAUAUGUCGUCGCUAAGCAUUUACA----UACUUAUA----CUA------------CA-----
.(((((((....((((.........))))......((.....)).)))(((((.((.....)).))))).)))).......----........----...------------..----- ( -18.00)
>DroGri_CAF1 24360 110 - 1
GGCUUGCCAACGGUGCAUAAAAAACGUACAACAAAUCAGAAAGAAGGUGCGACAGCAAUAUGUCGUCGCUAAGCAUUUACAUACAUACUUAUA----CUAAA----AGA-AAAAAAAAA
.(((((((....((((.........))))......((.....)).)))(((((.((.....)).))))).))))...................----.....----...-......... ( -18.00)
>DroYak_CAF1 49693 106 - 1
GGCUUGCCGACGGUGCAUAAAAAACGAACAACAAAUCAGAAAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGCAUUUAUUU----A-UCAUA----CUAAACAAAACCGAAA----AA
.(((((.((((...((((.......((........)).........))))(((((....))))))))).)))))........----.-.....----................----.. ( -18.59)
>DroMoj_CAF1 72125 101 - 1
GGCAUGCCAACGGUGCAUAAAAAACGUACAACAAAUCAGAAAGAAGGUGCGACAGCAAUAUGUCGUCGCUAAGCAUUUACA----UACUUAUA----CUACA----AAA-UACA-----
.((..(((....((((.........))))......((.....)).)))(((((.((.....)).)))))...)).......----........----.....----...-....----- ( -16.50)
>DroAna_CAF1 38532 109 - 1
GGGUUGCCAACGGUGCAUAAAAAACGAACAACAAAUCAGAAAGAAGGUGCGACAACAAAUUGUCGUCGCUAAGAAUUUAUUU----C-ACAUACGUACUAAA----AAA-AAAACCAAA
.((((......(((((.............................((((((((((....)))))).))))..(((.....))----)-......)))))...----...-..))))... ( -20.44)
>consensus
GGCUUGCCAACGGUGCAUAAAAAACGAACAACAAAUCAGAAAGAAGGUGCGACAACAAAAUGUCGUCGCUAAGCAUUUACAU____A_UCAUA____CUAAA____AAA_AAAA___AA
((....))...(((((...................((.....)).(((((((((......))))).))))..))))).......................................... (-14.55 = -14.72 +   0.17)

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 10:04:01 2006