Locus 2026

Sequence ID 2L_DroMel_CAF1
Location 5,482,709 – 5,482,865
Length 156
Max. P 0.928070
window3260 window3261 window3262

overview

Window 0

Location 5,482,709 – 5,482,805
Length 96
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -19.94
Consensus MFE -15.62
Energy contribution -15.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.78
SVM decision value 0.03
SVM RNA-class probability 0.550824
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5482709 96 + 22407834
UUUUUUUUGCCGCAUUCUUUUUUUUUAUU---UUUUCAUGGGGCAGCGGUCGCGCUGAAACGGAACCGCAAAUUAUUUUAAUUUGCGUUAAAUAAUGCA
...........(((((.(((.........---..(((.((...(((((....)))))...))))).(((((((((...)))))))))..))).))))). ( -21.70)
>DroSec_CAF1 101885 89 + 1
----UUUUGCCGCAUUUUUUUUU------UUAUUUUCUUGGGGCAGCGGCCGCGCUGAAACGGAACCGCAAAUUAUUUUAAUUUGCGUUAAAUAAUGCA
----.......(((((.(((...------.....((((.(...(((((....)))))...))))).(((((((((...)))))))))..))).))))). ( -21.90)
>DroEre_CAF1 103131 84 + 1
-----UUU-CCAUAUAUAC--------U-UUUUUUUCUUGGGGCAGCGGCCGCGCUGAAACGGAACCGCAAAUUAUUUUAAUUUGCGUUAAAUAAUGCA
-----.((-((.......(--------(-((........))))(((((....)))))....)))).(((((((((...)))))))))............ ( -18.20)
>DroYak_CAF1 110512 93 + 1
-----UUUACCAUAUAUCUUUCUUUCUU-UUUUUUUCUUGGGGCAGCGGCCGCGCUGAAACGGAACCGCAAAUUAUUUUAAUUUGCGUUAAAUAAUGCA
-----......................(-((..((((.((.(((....))).))..))))..))).(((((((((...)))))))))............ ( -17.10)
>DroAna_CAF1 109526 81 + 1
----UUC--------UUUUCUUA------UUGUUGUGUUGGGGCAGCGGCCGCGCUGAAACGGAACCGCAAAUUAUUUUAAUUUGCGUUAAAUAAUGCA
----...--------.....(((------(((((.((((....(((((....))))).)))).)))(((((((((...)))))))))...))))).... ( -20.80)
>consensus
____UUUU_CCACAUUUUUUUUU____U_UUUUUUUCUUGGGGCAGCGGCCGCGCUGAAACGGAACCGCAAAUUAUUUUAAUUUGCGUUAAAUAAUGCA
......................................((...(((((....)))))...))....(((((((((...)))))))))............ (-15.62 = -15.62 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,482,709 – 5,482,805
Length 96
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -18.36
Consensus MFE -16.10
Energy contribution -15.94
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.88
SVM decision value 1.19
SVM RNA-class probability 0.928070
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5482709 96 - 22407834
UGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGUUUCAGCGCGACCGCUGCCCCAUGAAAA---AAUAAAAAAAAAGAAUGCGGCAAAAAAAA
.((..........((((((((...))))))))((((.(((....))).))))))((((.(((.....---..............))).))))....... ( -22.11)
>DroSec_CAF1 101885 89 - 1
UGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGUUUCAGCGCGGCCGCUGCCCCAAGAAAAUAA------AAAAAAAAAUGCGGCAAAA----
.((..........((((((((...))))))))(((..(((....)))..)))))((((.((.........------.........)).))))...---- ( -19.97)
>DroEre_CAF1 103131 84 - 1
UGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGUUUCAGCGCGGCCGCUGCCCCAAGAAAAAAA-A--------GUAUAUAUGG-AAA-----
............(((((((((...))))))))).((((((..(((((....)))))..............-.--------......))))-)).----- ( -17.20)
>DroYak_CAF1 110512 93 - 1
UGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGUUUCAGCGCGGCCGCUGCCCCAAGAAAAAAA-AAGAAAGAAAGAUAUAUGGUAAA-----
(((..(((((..(((((((((...))))))))).(((.....(((((....)))))......))).....-.........)))))....)))..----- ( -16.50)
>DroAna_CAF1 109526 81 - 1
UGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGUUUCAGCGCGGCCGCUGCCCCAACACAACAA------UAAGAAAA--------GAA----
.((..........((((((((...))))))))(((..(((....)))..)))))................------........--------...---- ( -16.00)
>consensus
UGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGUUUCAGCGCGGCCGCUGCCCCAAGAAAAAAA_A____AAAAAAAAAUACGG_AAAA____
.((..........((((((((...))))))))(((..(((....)))..)))))............................................. (-16.10 = -15.94 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,482,765 – 5,482,865
Length 100
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 74.76
Mean single sequence MFE -17.81
Consensus MFE -11.05
Energy contribution -11.55
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.62
SVM decision value 1.03
SVM RNA-class probability 0.903297
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5482765 100 - 22407834
CA-----------UCUCUCCAACUCUCCGC------CG-UUUGCUUUGAGAAAUGCUCUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
..-----------......((((.....((------..-...))..(((((((............)))))))....))))..........(((((((((...)))))))))....... ( -16.90)
>DroVir_CAF1 148926 90 - 1
CA-----------UUUC---AUUUC--------------AAUUCAUUCAGCAAUGCUUUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
..-----------....---.....--------------..........((((((....................)))))).........(((((((((...)))))))))....... ( -12.95)
>DroPse_CAF1 120941 117 - 1
CACUCUCUCGCUCUCGCUCCCGCUCUCCGAAGCUGACG-CUGACGCUGAGAAAUGCUCUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
.........(((.(((...........)))))).((((-(.((((.(((((((............)))))))...)))))).........(((((((((...)))))))))))).... ( -22.70)
>DroWil_CAF1 149121 91 - 1
UU-----------CUUCUACAACUCA--------------UUGC-UUGA-AAAAGCUCUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
..-----------.............--------------..((-((..-..))))...............(((..((((.......))))((((((((...)))))))))))..... ( -14.00)
>DroAna_CAF1 109567 95 - 1
-----------------CUCACCUCUCUGA------CUGAAGACUCUGAGAAAGGCUCUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
-----------------............(------(.(((((...(((((((((........)))))))))..))..............(((((((((...))))))))).))).)) ( -16.60)
>DroPer_CAF1 121686 111 - 1
CACUCUCUCGCUCUCG------CUCUCCGAAGCUGACG-CUGACGCUGAGAAAUGCUCUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
.........(((.(((------.....)))))).((((-(.((((.(((((((............)))))))...)))))).........(((((((((...)))))))))))).... ( -23.70)
>consensus
CA___________UCUCU_CAACUCUCCGA______CG_AUGACGCUGAGAAAUGCUCUUAAUUUUUUCUCACCUCGUUGCAUUAUUUAACGCAAAUUAAAAUAAUUUGCGGUUCCGU
..............................................(((((((............)))))))..................(((((((((...)))))))))....... (-11.05 = -11.55 +   0.50)

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 10:17:28 2006