Locus 6435

Sequence ID 3R_DroMel_CAF1
Location 16,857,558 – 16,857,718
Length 160
Max. P 0.998416
window10487 window10488 window10489

overview

Window 7

Location 16,857,558 – 16,857,678
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -34.95
Consensus MFE -32.27
Energy contribution -32.35
Covariance contribution 0.08
Combinations/Pair 1.02
Mean z-score -1.38
Structure conservation index 0.92
SVM decision value 1.16
SVM RNA-class probability 0.924363
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16857558 120 - 27905053
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGUUGGCCUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUAGUCGCUGCCAUGAAC
..(((((((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))))(((.((.((((((...)))))...).)).))).)))).. ( -34.00)
>DroVir_CAF1 11098 120 - 1
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGUUGGCCUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUGGUCGCUGCCAUGAAU
..(((((((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))))(((.(((((((((...))))..))).)).))).)))).. ( -34.40)
>DroPse_CAF1 18902 120 - 1
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGCUGGACUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUAGUCGCUGCCAUGAAU
..(((((((.((((((((.((.((((..((.(((.((.((((.....)))))).))).))..)))).)).)))))))))))(((.((.((((((...)))))...).)).))).)))).. ( -36.70)
>DroGri_CAF1 12733 120 - 1
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCAAUCAAGGCCUGGCCUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUAGUCGCUGCCAUGAAU
..(((((((.((((((((.((.((((..((.((..((.(((......))).))..)).))..)))).)).)))))))))))(((.((.((((((...)))))...).)).))).)))).. ( -33.90)
>DroYak_CAF1 12566 120 - 1
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGUUGGCCUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUAGUCGCUGCCAUGAAC
..(((((((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))))(((.((.((((((...)))))...).)).))).)))).. ( -34.00)
>DroPer_CAF1 19505 120 - 1
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGCUGGACUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUAGUCGCUGCCAUGAAU
..(((((((.((((((((.((.((((..((.(((.((.((((.....)))))).))).))..)))).)).)))))))))))(((.((.((((((...)))))...).)).))).)))).. ( -36.70)
>consensus
UGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGCUGGCCUGAGCUUCACAAACUCCUUCAGGAAGCAAUGUCAUCGUAUAAUGAUCUAGUCGCUGCCAUGAAU
..(((((((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))))(((.((.((((((...)))))...).)).))).)))).. (-32.27 = -32.35 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,857,598 – 16,857,718
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.33
Mean single sequence MFE -38.35
Consensus MFE -32.67
Energy contribution -32.87
Covariance contribution 0.20
Combinations/Pair 1.02
Mean z-score -2.62
Structure conservation index 0.85
SVM decision value 1.84
SVM RNA-class probability 0.979394
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16857598 120 + 27905053
UCCUGAAGGAGUUUGUGAAGCUCAGGCCAACCCUUGAUGGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAAAUAUUCGGCUUGUCGAAUAUGACGGACUCGUCAAUU
(((((.(((((((.((((..((.((..((.(((.....)))..))..)).))..)))).))))))).))).))..(((((((..((((((((....)))))))).....))).))))... ( -38.90)
>DroVir_CAF1 11138 120 + 1
UCCUGAAGGAGUUUGUGAAGCUCAGGCCAACCCUUGAUGGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAAAUAUUCGGUUUGUCGAAUAUAACAGAUUCGUCAAUU
(((((.(((((((.((((..((.((..((.(((.....)))..))..)).))..)))).))))))).))).))..(((((((..((((((((....)))))))).....))).))))... ( -34.40)
>DroPse_CAF1 18942 120 + 1
UCCUGAAGGAGUUUGUGAAGCUCAGUCCAGCCCUUGAUGGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAGAUAUUCGGCUUGUCGAAUAUAACGGAUUCGUCAAUU
(((((.(((((((.((((..((.(((.((((((.....)))).)).))).))..)))).))))))).))).))..(((((((..((((((((....)))))))).....))).))))... ( -41.50)
>DroGri_CAF1 12773 120 + 1
UCCUGAAGGAGUUUGUGAAGCUCAGGCCAGGCCUUGAUUGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAAAUAUUCGGCUUGUCGAAUAUCACGGAUUCGUCAAUU
(((((.(((((((.((((..((.((..((.(((......))).))..)).))..)))).))))))).))).))..(((((((..((((((((....)))))))).....))).))))... ( -37.60)
>DroYak_CAF1 12606 120 + 1
UCCUGAAGGAGUUUGUGAAGCUCAGGCCAACCCUUGAUGGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAAAUAUUCGGCUUGUCGAAUAUGACGGAUUCGUCUAUU
(((((.(((((((.((((..((.((..((.(((.....)))..))..)).))..)))).))))))).))).))...........((((((((....))))))))((((....)))).... ( -36.20)
>DroPer_CAF1 19545 120 + 1
UCCUGAAGGAGUUUGUGAAGCUCAGUCCAGCCCUUGAUGGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAGAUAUUCGGCUUGUCGAAUAUAACGGAUUCGUCAAUU
(((((.(((((((.((((..((.(((.((((((.....)))).)).))).))..)))).))))))).))).))..(((((((..((((((((....)))))))).....))).))))... ( -41.50)
>consensus
UCCUGAAGGAGUUUGUGAAGCUCAGGCCAACCCUUGAUGGGCAUGUACUUAGGAUCACCAAUUCCUCCAGCGAAAUGACAGUAAAUAUUCGGCUUGUCGAAUAUAACGGAUUCGUCAAUU
(((((.(((((((.((((..((.((..((..(((....)))..))..)).))..)))).))))))).))).))..(((((((..((((((((....)))))))).....))).))))... (-32.67 = -32.87 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,857,598 – 16,857,718
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -37.77
Consensus MFE -33.51
Energy contribution -33.45
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -2.83
Structure conservation index 0.89
SVM decision value 3.09
SVM RNA-class probability 0.998416
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16857598 120 - 27905053
AAUUGACGAGUCCGUCAUAUUCGACAAGCCGAAUAUUUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGUUGGCCUGAGCUUCACAAACUCCUUCAGGA
...(((((....)))))((((((......))))))............((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))) ( -37.50)
>DroVir_CAF1 11138 120 - 1
AAUUGACGAAUCUGUUAUAUUCGACAAACCGAAUAUUUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGUUGGCCUGAGCUUCACAAACUCCUUCAGGA
...(((((.....((.(((((((......)))))))..)))))))..((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))) ( -36.30)
>DroPse_CAF1 18942 120 - 1
AAUUGACGAAUCCGUUAUAUUCGACAAGCCGAAUAUCUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGCUGGACUGAGCUUCACAAACUCCUUCAGGA
...(((((.....((.(((((((......)))))))..)))))))..((.((((((((.((.((((..((.(((.((.((((.....)))))).))).))..)))).)).)))))))))) ( -38.90)
>DroGri_CAF1 12773 120 - 1
AAUUGACGAAUCCGUGAUAUUCGACAAGCCGAAUAUUUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCAAUCAAGGCCUGGCCUGAGCUUCACAAACUCCUUCAGGA
...(((((.....((((((((((......)))))).)))))))))..((.((((((((.((.((((..((.((..((.(((......))).))..)).))..)))).)).)))))))))) ( -37.40)
>DroYak_CAF1 12606 120 - 1
AAUAGACGAAUCCGUCAUAUUCGACAAGCCGAAUAUUUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGUUGGCCUGAGCUUCACAAACUCCUUCAGGA
....((((....))))(((((((......)))))))...........((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))) ( -37.60)
>DroPer_CAF1 19545 120 - 1
AAUUGACGAAUCCGUUAUAUUCGACAAGCCGAAUAUCUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGCUGGACUGAGCUUCACAAACUCCUUCAGGA
...(((((.....((.(((((((......)))))))..)))))))..((.((((((((.((.((((..((.(((.((.((((.....)))))).))).))..)))).)).)))))))))) ( -38.90)
>consensus
AAUUGACGAAUCCGUUAUAUUCGACAAGCCGAAUAUUUACUGUCAUUUCGCUGGAGGAAUUGGUGAUCCUAAGUACAUGCCCAUCAAGGGCUGGCCUGAGCUUCACAAACUCCUUCAGGA
....((((....))))(((((((......)))))))...........((.((((((((.((.((((..((.((..((.((((.....))))))..)).))..)))).)).)))))))))) (-33.51 = -33.45 +  -0.06)

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 12:21:29 2006