Locus 2347

Sequence ID 2L_DroMel_CAF1
Location 6,360,569 – 6,360,706
Length 137
Max. P 0.991941
window3783 window3784 window3785 window3786

overview

Window 3

Location 6,360,569 – 6,360,677
Length 108
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 72.54
Mean single sequence MFE -35.54
Consensus MFE -10.88
Energy contribution -13.44
Covariance contribution 2.56
Combinations/Pair 1.11
Mean z-score -2.00
Structure conservation index 0.31
SVM decision value 1.10
SVM RNA-class probability 0.915754
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6360569 108 + 22407834
-----GCAAAUACGGG---CGAGUUAUAGGAUCCGUGCUCUCGGUGGGGUAACCG-CCAAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGUUCUGUUCCCAGCCGCCCC-CAUUUGG
-----.(((((..(((---((.(((((((((((.(((((...(((((.....)))-)).)))))((.(((((....))))).)).....))))))))....)))))))).-.))))). ( -36.30)
>DroSec_CAF1 8308 108 + 1
-----GCAAAUACGGG---CGAGUUAUAGGAUCCGUGCUCUCGGUGGGGUAACCG-CCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGUUCGGUUCCCAGCCGCCCC-CAUUUGG
-----.(((((..(((---((.(((...(((.(((.((.((((((((.....)))-))))).))((.(((((....))))).)).........))).))).)))))))).-.))))). ( -41.30)
>DroEre_CAF1 8132 101 + 1
-----GCAAAUACGGG---CGAGUUAUGGGAUCCGUGCUCUCGGUGGGGUAACCG-CCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGU-----UCCCAGCCGCCCC-CAUU--G
-----........(((---((.((..(((((.(((.((.((((((((.....)))-))))).))((.(((((....))))).))....))).-----)))))))))))).-....--. ( -42.50)
>DroWil_CAF1 23025 97 + 1
UAUUUGAGAGUGAAAG---UGAGGAGCCAAAUCCA--CCCGCAGUU-GGUAACCAAACACAUGCGGUAAUUUACCUAAUUUUCAACGC---UUC---UCCC----CCUCA-CAU----
.........((((..(---.(((((((........--.(((((.((-((...)))).....))))).((((.....))))......))---)))---)).)----..)))-)..---- ( -23.00)
>DroYak_CAF1 8473 104 + 1
--------AAAGCGGGAUAGGAGUUAUUGGAUCCCUGCUCUCGGUGGGGUAACCG-CCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGC-----UCGCAGCCGCCCCCCAUUUGG
--------.....(((....(((..(((((((....((.((((((((.....)))-))))).))........))))))).))).....((((-----.....))))...)))...... ( -34.60)
>consensus
_____GCAAAUACGGG___CGAGUUAUAGGAUCCGUGCUCUCGGUGGGGUAACCG_CCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGUUC___UCCCAGCCGCCCC_CAUUUGG
.............(((....((((............)))).((((.(((.......((((.((.((.(((((....))))).)).)))))).......))).)))))))......... (-10.88 = -13.44 +   2.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,360,569 – 6,360,677
Length 108
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 72.54
Mean single sequence MFE -36.66
Consensus MFE -12.36
Energy contribution -12.16
Covariance contribution -0.20
Combinations/Pair 1.40
Mean z-score -2.39
Structure conservation index 0.34
SVM decision value 2.30
SVM RNA-class probability 0.991941
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6360569 108 - 22407834
CCAAAUG-GGGGCGGCUGGGAACAGAACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUUGG-CGGUUACCCCACCGAGAGCACGGAUCCUAUAACUCG---CCCGUAUUUGC-----
.((((((-.(((((((((....)))..(((....((.(((((....))))).))((.(((((-.((.....)).))))).)).)))..........)))---))).)))))).----- ( -38.00)
>DroSec_CAF1 8308 108 - 1
CCAAAUG-GGGGCGGCUGGGAACCGAACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGG-CGGUUACCCCACCGAGAGCACGGAUCCUAUAACUCG---CCCGUAUUUGC-----
.((((((-.((((((.(((((.(((.........((.(((((....))))).))((.(((((-.((.....)).))))).)).))).)))))....)))---))).)))))).----- ( -42.20)
>DroEre_CAF1 8132 101 - 1
C--AAUG-GGGGCGGCUGGGA-----ACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGG-CGGUUACCCCACCGAGAGCACGGAUCCCAUAACUCG---CCCGUAUUUGC-----
.--((((-.((((((.(((((-----.(((....((.(((((....))))).))((.(((((-.((.....)).))))).)).))).)))))....)))---))).))))...----- ( -40.70)
>DroWil_CAF1 23025 97 - 1
----AUG-UGAGG----GGGA---GAA---GCGUUGAAAAUUAGGUAAAUUACCGCAUGUGUUUGGUUACC-AACUGCGGG--UGGAUUUGGCUCCUCA---CUUUCACUCUCAAAUA
----..(-(((((----(.((---(.(---((..(....).....((((((.(((((.((...(((...))-)))))))).--..))))))))).))).---)))))))......... ( -26.00)
>DroYak_CAF1 8473 104 - 1
CCAAAUGGGGGGCGGCUGCGA-----GCCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGG-CGGUUACCCCACCGAGAGCAGGGAUCCAAUAACUCCUAUCCCGCUUU--------
.....(((((((..(((((((-----((.....(((.(((((....))))).))).)))).)-))))..)))).)))(((((.(((((............))))))))))-------- ( -36.40)
>consensus
CCAAAUG_GGGGCGGCUGGGA___GAACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGG_CGGUUACCCCACCGAGAGCACGGAUCCUAUAACUCG___CCCGUAUUUGC_____
.........(((..((((..................................))))((((...((((......)))).))))....................)))............. (-12.36 = -12.16 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,360,601 – 6,360,706
Length 105
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 90.05
Mean single sequence MFE -33.78
Consensus MFE -24.24
Energy contribution -25.55
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.72
SVM decision value 0.27
SVM RNA-class probability 0.660280
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6360601 105 + 22407834
UCGGUGGGGUAACCGCCAAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGUUCUGUUCCCAGCCGCCCC-CAUUUGG-GAUACUGAUUGGAUUUCAGUAUUGUUCCU
.((((((((.(((((....(((.((.(((((....))))).)).))))))))....))))).)))..((-(....))-)(((((((.......)))))))....... ( -28.00)
>DroSec_CAF1 8340 101 + 1
UCGGUGGGGUAACCGCCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGUUCGGUUCCCAGCCGCCCC-CAUUUGG-GG----GAUUGGAUUUCAGUAUUGUUCCU
.((((.(((.(((((((((.((.((.(((((....))))).)).))))))..)))))))).))))((((-(....))-))----)...(((............))). ( -36.70)
>DroEre_CAF1 8164 99 + 1
UCGGUGGGGUAACCGCCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGU-----UCCCAGCCGCCCC-CAUU--GGGGUGCUGAUUGGAUUUCAGUACUGUUCCU
(((((((.....)))))))(..(((......((((((((..(......(((-----.....)))(((((-....--))))))..))))))))..)))..)....... ( -33.10)
>DroYak_CAF1 8505 102 + 1
UCGGUGGGGUAACCGCCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGC-----UCGCAGCCGCCCCCCAUUUGGGGGUACUGAUUGGAUUUCAGUAUUGUUCCU
(((((((.....)))))))..((((......((((((((.........(((-----.....)))((((((.....))))))...))))))))..))))......... ( -37.30)
>consensus
UCGGUGGGGUAACCGCCGAGCGCUGUAAAUUAUCUAAUUUUCAAUGUCGGU_____UCCCAGCCGCCCC_CAUUUGG_GGUACUGAUUGGAUUUCAGUAUUGUUCCU
(((((((.....)))))))..((((......((((((((........(((((........)))))((((......)))).....))))))))..))))......... (-24.24 = -25.55 +   1.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,360,601 – 6,360,706
Length 105
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 90.05
Mean single sequence MFE -30.20
Consensus MFE -22.14
Energy contribution -23.57
Covariance contribution 1.44
Combinations/Pair 1.07
Mean z-score -1.97
Structure conservation index 0.73
SVM decision value 0.37
SVM RNA-class probability 0.708943
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6360601 105 - 22407834
AGGAACAAUACUGAAAUCCAAUCAGUAUC-CCAAAUG-GGGGCGGCUGGGAACAGAACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUUGGCGGUUACCCCACCGA
.((....(((((((.......))))))).-.....((-(((....(((....)))(((((.(((((.(((((....))))).)))....)).))))).))))))).. ( -27.80)
>DroSec_CAF1 8340 101 - 1
AGGAACAAUACUGAAAUCCAAUC----CC-CCAAAUG-GGGGCGGCUGGGAACCGAACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGGCGGUUACCCCACCGA
.(((............)))...(----((-((....)-))))(((..((((((((..(((((.(((.(((((....))))).))).).))))))))).)))..))). ( -33.80)
>DroEre_CAF1 8164 99 - 1
AGGAACAGUACUGAAAUCCAAUCAGCACCCC--AAUG-GGGGCGGCUGGGA-----ACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGGCGGUUACCCCACCGA
.((....((((((...(((...((((.((((--....-))))..)))))))-----.(((((.(((.(((((....))))).))).).))))))).)))....)).. ( -26.40)
>DroYak_CAF1 8505 102 - 1
AGGAACAAUACUGAAAUCCAAUCAGUACCCCCAAAUGGGGGGCGGCUGCGA-----GCCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGGCGGUUACCCCACCGA
.((.....((((((.......))))))...))...(((((((..(((((((-----((.....(((.(((((....))))).))).)))).)))))..)))).))). ( -32.80)
>consensus
AGGAACAAUACUGAAAUCCAAUCAGUACC_CCAAAUG_GGGGCGGCUGGGA_____ACCGACAUUGAAAAUUAGAUAAUUUACAGCGCUCGGCGGUUACCCCACCGA
.((....(((((((.......)))))))..........((((..((((.........(((((.(((.(((((....))))).))).).))))))))..)))).)).. (-22.14 = -23.57 +   1.44)

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 10:25:54 2006