Locus 852

Sequence ID 3R_DroMel_CAF1
Location 2,889,408 – 2,889,568
Length 160
Max. P 0.984373
window1358 window1359 window1360 window1361

overview

Window 8

Location 2,889,408 – 2,889,528
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.72
Mean single sequence MFE -27.77
Consensus MFE -18.40
Energy contribution -21.07
Covariance contribution 2.67
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.66
SVM decision value 1.33
SVM RNA-class probability 0.942690
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2889408 120 + 27905053
UAGCAAAUCUGCUCCAGUAGCUAAAACGGAUGUCAAAGAGAACAUCAAACAGGAGGUAAAGAAGGAGGUGAAGAAGGAGAUCGCUAAAACGCCAUCUCCGCCUCCUGCCCAACCACCAAA
((((....(((...)))..)))).....(((((........))))).....((.(((.....(((((((......((((((.((......)).))))))))))))).....))).))... ( -35.30)
>DroSec_CAF1 1352 109 + 1
-----------CUCCAGUAGCUAAAACAAAUGUAAAAGAGAAUAUCAAACAGGAGGUAAAGAAGGAGGUGAAGAAGGAGAUCGCUAAAACGCCAUCUCCGCCUCCUGCCCAACCACCAAA
-----------........................................((.(((.....(((((((......((((((.((......)).))))))))))))).....))).))... ( -27.90)
>DroEre_CAF1 2925 108 + 1
AAGCAAAUCUGCACAAGUAGCUAAAGCGGCUGUAAAAGAGAAUAUCAAACAGGAGGUCA------------AGAAGGAGAUUGCUAAAACGCCACCUCCGCCUGCUCCCCAACCACCAAA
.......(((.....(((.((....)).))).....)))............((.((...------------((..((((...((......))...))))..))...)))).......... ( -20.10)
>consensus
_AGCAAAUCUGCUCCAGUAGCUAAAACGGAUGUAAAAGAGAAUAUCAAACAGGAGGUAAAGAAGGAGGUGAAGAAGGAGAUCGCUAAAACGCCAUCUCCGCCUCCUGCCCAACCACCAAA
...................................................((.(((.....(((((((......((((((.((......)).))))))))))))).....))).))... (-18.40 = -21.07 +   2.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,889,408 – 2,889,528
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.72
Mean single sequence MFE -35.17
Consensus MFE -26.26
Energy contribution -26.82
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.39
Structure conservation index 0.75
SVM decision value 1.95
SVM RNA-class probability 0.983743
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2889408 120 - 27905053
UUUGGUGGUUGGGCAGGAGGCGGAGAUGGCGUUUUAGCGAUCUCCUUCUUCACCUCCUUCUUUACCUCCUGUUUGAUGUUCUCUUUGACAUCCGUUUUAGCUACUGGAGCAGAUUUGCUA
.(..((((((((((((((((.((((((.((......)).))))))...................))))))))..((((((......))))))....))))))))..)(((......))). ( -40.85)
>DroSec_CAF1 1352 109 - 1
UUUGGUGGUUGGGCAGGAGGCGGAGAUGGCGUUUUAGCGAUCUCCUUCUUCACCUCCUUCUUUACCUCCUGUUUGAUAUUCUCUUUUACAUUUGUUUUAGCUACUGGAG-----------
((..(((((..(((((((((.((((((.((......)).))))))...................)))))))))..)......((...((....))...))))))..)).----------- ( -33.35)
>DroEre_CAF1 2925 108 - 1
UUUGGUGGUUGGGGAGCAGGCGGAGGUGGCGUUUUAGCAAUCUCCUUCU------------UGACCUCCUGUUUGAUAUUCUCUUUUACAGCCGCUUUAGCUACUUGUGCAGAUUUGCUU
...(((((((((((((((((.((((((.((......)).))))))..))------------))..)))))....((.....)).....))))))))...((.......)).......... ( -31.30)
>consensus
UUUGGUGGUUGGGCAGGAGGCGGAGAUGGCGUUUUAGCGAUCUCCUUCUUCACCUCCUUCUUUACCUCCUGUUUGAUAUUCUCUUUUACAUCCGUUUUAGCUACUGGAGCAGAUUUGCU_
((..(((((..(((((((((.((((((.((......)).))))))...................)))))))))..))................((....)))))..))............ (-26.26 = -26.82 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,889,448 – 2,889,568
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.44
Mean single sequence MFE -26.26
Consensus MFE -18.40
Energy contribution -21.07
Covariance contribution 2.67
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.70
SVM decision value 1.97
SVM RNA-class probability 0.984373
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2889448 120 + 27905053
AACAUCAAACAGGAGGUAAAGAAGGAGGUGAAGAAGGAGAUCGCUAAAACGCCAUCUCCGCCUCCUGCCCAACCACCAAAAGCUGCUAAUCCAUCCCCUCCACCAUCUAAAGCCGCACCA
...........((.(((.....(((((((......((((((.((......)).))))))))))))).....))).))....((.(((.......................))).)).... ( -31.40)
>DroSec_CAF1 1381 115 + 1
AAUAUCAAACAGGAGGUAAAGAAGGAGGUGAAGAAGGAGAUCGCUAAAACGCCAUCUCCGCCUCCUGCCCAACCACCAAAAGCUGCUAGUCCAUCCCCUCCACCAUCUAAAGCCC-----
...........((.(((.....(((((((......((((((.((......)).))))))))))))).....))).))....(((..(((.................))).)))..----- ( -30.13)
>DroEre_CAF1 2965 96 + 1
AAUAUCAAACAGGAGGUCA------------AGAAGGAGAUUGCUAAAACGCCACCUCCGCCUGCUCCCCAACCACCAAAAGCUGCUAAUCCAUCCCC---ACCGCCAGCA---------
...........((.((...------------((..((((...((......))...))))..))...))))...........(((((............---...).)))).--------- ( -17.26)
>consensus
AAUAUCAAACAGGAGGUAAAGAAGGAGGUGAAGAAGGAGAUCGCUAAAACGCCAUCUCCGCCUCCUGCCCAACCACCAAAAGCUGCUAAUCCAUCCCCUCCACCAUCUAAAGCC______
...........((.(((.....(((((((......((((((.((......)).))))))))))))).....))).))........................................... (-18.40 = -21.07 +   2.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,889,448 – 2,889,568
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -38.60
Consensus MFE -28.45
Energy contribution -28.57
Covariance contribution 0.12
Combinations/Pair 1.14
Mean z-score -1.77
Structure conservation index 0.74
SVM decision value 0.77
SVM RNA-class probability 0.846147
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2889448 120 - 27905053
UGGUGCGGCUUUAGAUGGUGGAGGGGAUGGAUUAGCAGCUUUUGGUGGUUGGGCAGGAGGCGGAGAUGGCGUUUUAGCGAUCUCCUUCUUCACCUCCUUCUUUACCUCCUGUUUGAUGUU
....(((....(((..((((((((((..((.....(((((......)))))....(((((.((((((.((......)).)))))).))))).))..))))))))))..))).....))). ( -42.40)
>DroSec_CAF1 1381 115 - 1
-----GGGCUUUAGAUGGUGGAGGGGAUGGACUAGCAGCUUUUGGUGGUUGGGCAGGAGGCGGAGAUGGCGUUUUAGCGAUCUCCUUCUUCACCUCCUUCUUUACCUCCUGUUUGAUAUU
-----......(((..((((((((((..((.(((((.((.....)).)))))...(((((.((((((.((......)).)))))).))))).))..))))))))))..)))......... ( -42.90)
>DroEre_CAF1 2965 96 - 1
---------UGCUGGCGGU---GGGGAUGGAUUAGCAGCUUUUGGUGGUUGGGGAGCAGGCGGAGGUGGCGUUUUAGCAAUCUCCUUCU------------UGACCUCCUGUUUGAUAUU
---------.((.((.(((---.((((.......((.((((((.(....).))))))..))((((((.((......)).)))))).)))------------).))).)).))........ ( -30.50)
>consensus
______GGCUUUAGAUGGUGGAGGGGAUGGAUUAGCAGCUUUUGGUGGUUGGGCAGGAGGCGGAGAUGGCGUUUUAGCGAUCUCCUUCUUCACCUCCUUCUUUACCUCCUGUUUGAUAUU
...........(((((((....((((.........(((((......)))))....(((((.((((((.((......)).)))))).))))).............)))))))))))..... (-28.45 = -28.57 +   0.12)

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 09:53:50 2006