Locus 1813

Sequence ID 3L_DroMel_CAF1
Location 5,098,794 – 5,098,947
Length 153
Max. P 0.995708
window2823 window2824 window2825 window2826

overview

Window 3

Location 5,098,794 – 5,098,908
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.99
Mean single sequence MFE -23.42
Consensus MFE -20.30
Energy contribution -20.80
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.87
SVM decision value 0.44
SVM RNA-class probability 0.738217
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5098794 114 + 23771897
CAAGAUGAACAA------GUUUGUCUUGCAGCAAAGAUGUUUACCGACUGCCAAUGCAAAAAAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACAAAAUGGCAAACGUUUCCCAG
(((((..((...------.))..)))))......((((((((.(((...(((........................)))((((((....))))))........))).))))))))..... ( -25.86)
>DroSec_CAF1 291867 113 + 1
CAAGAUGUACAA------GUUUGUCUUGCAGCAAAGAUGUUUACCGACUGCCAAUGCAAA-AAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACAAAAUGGCAAACGUUUUCCAG
(((((((.....------...))))))).....(((((((((.(((...(((........-...............)))((((((....))))))........))).))))))))).... ( -24.10)
>DroSim_CAF1 313519 104 + 1
---------CAA------GUUUGUCUUGCAGCAAAGAUGUUUACCGACUGCCAAUGCAAA-AAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACGAAAUGGCAAACGUUUUCCAG
---------...------(((((((..((.....(((((.........(((....)))..-......))))).....))((((((....)))))).........)))))))......... ( -21.83)
>DroYak_CAF1 304128 118 + 1
CUAGAUGUACAAGUACGAGUAUGUCUUGCAGCAAAGAUGUUUACCGACUGCCAAUGCAAA-AAAUAUCAUUUAAAUGGCAUCACCAAAUGGAGAUACACA-AAUGGCAAACGUUUUCCAG
..((((((((........)))))))).......(((((((((.(((...((((.......-..............))))(((.((....)).))).....-..))).))))))))).... ( -21.90)
>consensus
CAAGAUGUACAA______GUUUGUCUUGCAGCAAAGAUGUUUACCGACUGCCAAUGCAAA_AAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACAAAAUGGCAAACGUUUUCCAG
..................(((((((..((...((((((((((......(((....)))...))))))).))).....))((((((....)))))).........)))))))......... (-20.30 = -20.80 +   0.50)

alignment

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secondary structure

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Window 4

Location 5,098,794 – 5,098,908
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.99
Mean single sequence MFE -28.73
Consensus MFE -23.33
Energy contribution -23.57
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.81
SVM decision value 0.88
SVM RNA-class probability 0.873493
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5098794 114 - 23771897
CUGGGAAACGUUUGCCAUUUUGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUUUUUUGCAUUGGCAGUCGGUAAACAUCUUUGCUGCAAGACAAAC------UUGUUCAUCUUG
...(....)(((((((.......((((((((....))))))))..................((((....))))..))))))).....((..(((((.....)------)))).))..... ( -29.10)
>DroSec_CAF1 291867 113 - 1
CUGGAAAACGUUUGCCAUUUUGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUU-UUUGCAUUGGCAGUCGGUAAACAUCUUUGCUGCAAGACAAAC------UUGUACAUCUUG
..(((....(((((((.......((((((((....))))))))................-.((((....))))..))))))).....((.((((((.....)------)))))))))).. ( -29.40)
>DroSim_CAF1 313519 104 - 1
CUGGAAAACGUUUGCCAUUUCGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUU-UUUGCAUUGGCAGUCGGUAAACAUCUUUGCUGCAAGACAAAC------UUG---------
.........(((((.(((((...((((((((....)))))))).....))))).....(-((((((...((((..(((....))).))))))))))))))))------...--------- ( -25.40)
>DroYak_CAF1 304128 118 - 1
CUGGAAAACGUUUGCCAUU-UGUGUAUCUCCAUUUGGUGAUGCCAUUUAAAUGAUAUUU-UUUGCAUUGGCAGUCGGUAAACAUCUUUGCUGCAAGACAUACUCGUACUUGUACAUCUAG
(((((....(((((((...-((.(((((.((....)).)))))))..............-.((((....))))..))))))).....((.((((((((......)).))))))))))))) ( -31.00)
>consensus
CUGGAAAACGUUUGCCAUUUUGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUU_UUUGCAUUGGCAGUCGGUAAACAUCUUUGCUGCAAGACAAAC______UUGUACAUCUUG
.........(((((((.....(.((((((((....))))))))).................((((....))))..))))))).((((......))))....................... (-23.33 = -23.57 +   0.25)

alignment

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secondary structure

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Window 5

Location 5,098,828 – 5,098,947
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.16
Mean single sequence MFE -29.42
Consensus MFE -24.31
Energy contribution -25.12
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.12
Structure conservation index 0.83
SVM decision value 0.95
SVM RNA-class probability 0.888266
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5098828 119 + 23771897
UUACCGACUGCCAAUGCAAAAAAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACAAAAUGGCAAACGUUUCCCAGGGGCAGUCAAGCGAUGUAAAAUAUUUGUA-UGGAGAGGUU
..((((((((((..((..(((.....((((((.....(.((((((....)))))).)...))))))......)))..))..)))))))..((((..........)))).-......))). ( -29.70)
>DroSec_CAF1 291901 118 + 1
UUACCGACUGCCAAUGCAAA-AAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACAAAAUGGCAAACGUUUUCCAGGGGCAGUCAAGCGAUGUAAAACAUAUGUA-CGGAGAGGUU
..((((((((((..((.(((-(....((((((.....(.((((((....)))))).)...))))))......)))).))..)))))))..((((((.....))).))).-......))). ( -31.60)
>DroSim_CAF1 313544 118 + 1
UUACCGACUGCCAAUGCAAA-AAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACGAAAUGGCAAACGUUUUCCAGCGGCAGUCAAGCGAUGUAAAAUAUAUGUA-CGGGGAGGUU
..((((((((((..((.(((-(....((((((.....(.((((((....)))))).)...))))))......)))).))..)))))))...(((((((.....))))).-))....))). ( -31.00)
>DroYak_CAF1 304168 118 + 1
UUACCGACUGCCAAUGCAAA-AAAUAUCAUUUAAAUGGCAUCACCAAAUGGAGAUACACA-AAUGGCAAACGUUUUCCAGUGGCAGUCAAGCGAUGUAAAAUAUGUGGAGUGGACAGAGG
...((((((((((.((.(((-(....((((((...((..(((.((....)).))).)).)-)))))......)))).)).))))))))...(.(((((...))))).)...))....... ( -25.40)
>consensus
UUACCGACUGCCAAUGCAAA_AAAUAUCAUUUAAAAGGCAUCUCCAAAUGGAGAUACACAAAAUGGCAAACGUUUUCCAGGGGCAGUCAAGCGAUGUAAAAUAUAUGUA_CGGAGAGGUU
...(((((((((..((.(((......((((((.....(.((((((....)))))).)...)))))).......))).))..)))))))..(((((((...)))).)))...))....... (-24.31 = -25.12 +   0.81)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,098,828 – 5,098,947
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.16
Mean single sequence MFE -32.30
Consensus MFE -29.58
Energy contribution -30.32
Covariance contribution 0.75
Combinations/Pair 1.06
Mean z-score -3.07
Structure conservation index 0.92
SVM decision value 2.61
SVM RNA-class probability 0.995708
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5098828 119 - 23771897
AACCUCUCCA-UACAAAUAUUUUACAUCGCUUGACUGCCCCUGGGAAACGUUUGCCAUUUUGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUUUUUUGCAUUGGCAGUCGGUAA
..........-.................(((.(((((((..((.((((....((.(((((.(.((((((((....)))))))))....))))).))...)))).))..)))))))))).. ( -32.00)
>DroSec_CAF1 291901 118 - 1
AACCUCUCCG-UACAUAUGUUUUACAUCGCUUGACUGCCCCUGGAAAACGUUUGCCAUUUUGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUU-UUUGCAUUGGCAGUCGGUAA
.(((.....(-((.........))).......(((((((..((.((((.((....(((((.(.((((((((....)))))))))....)))))..)).)-))).))..)))))))))).. ( -33.00)
>DroSim_CAF1 313544 118 - 1
AACCUCCCCG-UACAUAUAUUUUACAUCGCUUGACUGCCGCUGGAAAACGUUUGCCAUUUCGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUU-UUUGCAUUGGCAGUCGGUAA
.(((.....(-((.........))).......((((((((.((.((((.((....(((((...((((((((....)))))))).....)))))..)).)-))).)).))))))))))).. ( -33.60)
>DroYak_CAF1 304168 118 - 1
CCUCUGUCCACUCCACAUAUUUUACAUCGCUUGACUGCCACUGGAAAACGUUUGCCAUU-UGUGUAUCUCCAUUUGGUGAUGCCAUUUAAAUGAUAUUU-UUUGCAUUGGCAGUCGGUAA
............................(((.((((((((.((.((((.((....((((-((.(((((.((....)).)))))....))))))..)).)-))).)).))))))))))).. ( -30.60)
>consensus
AACCUCUCCA_UACAUAUAUUUUACAUCGCUUGACUGCCCCUGGAAAACGUUUGCCAUUUUGUGUAUCUCCAUUUGGAGAUGCCUUUUAAAUGAUAUUU_UUUGCAUUGGCAGUCGGUAA
............................(((.((((((((.((.(((.....((.(((((...((((((((....)))))))).....))))).))....))).)).))))))))))).. (-29.58 = -30.32 +   0.75)

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 10:17:20 2006