Locus 2103

Sequence ID 2R_DroMel_CAF1
Location 7,868,923 – 7,869,108
Length 185
Max. P 0.904562
window3483 window3484 window3485 window3486

overview

Window 3

Location 7,868,923 – 7,869,028
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 84.38
Mean single sequence MFE -26.60
Consensus MFE -18.30
Energy contribution -18.78
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.64
Structure conservation index 0.69
SVM decision value -0.01
SVM RNA-class probability 0.530217
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7868923 105 - 20766785
UCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAACGGAUGUUUAGCAUUCUGGUAAUAGUACUAUGGGUAGUAAAUGAAGUAAAUA
((((.((((.....))))..))))..((((((....(((((....)))))....(((((.....))))).........(((((....)))))...)))))).... ( -25.80)
>DroSim_CAF1 11589 105 - 1
UCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAAUGGAUGUUUAGCAUUCUGGUAAUAGUACUACGGGUAGUAAAUGAAAUAAAUA
((((.((((.....))))..))))..(((((((((((((((....)))))....(((((.....)))))(((((....)))))))))........)))))).... ( -26.80)
>DroEre_CAF1 12983 105 - 1
UCGGAUGGUAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAAUGGGUGUUUCGCAUUCUGGUAAUAGUACUAUGGGGAGUAAAUAAAAUAAAUG
((..((((((...(((((((.((((((((..((...(((((....)))))....))))))))))...)))))))....))))))..))................. ( -28.40)
>DroYak_CAF1 11868 105 - 1
UCUGAUGGUAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAACGGAUGUUUCGCAUUCUGGUAAUAGUACUAUGGGGAGUAAAUAAAAUAAAUA
(((.((((((...(((((((.((((((((((.....(((((....)))))....))))))))))...)))))))....)))))).)))................. ( -31.90)
>DroAna_CAF1 11226 98 - 1
UCAGAGGGCAGGAUUCCUGAUUGAAAAAUCUCUUCGGCCAUUGUGGUGCCAAACGGAUGUUUAGCAUUCUGGUUGUAAUACUGUAA-------AAUAAUUGUAAA
((((((.((..((((((.((((....)))).....((((......).)))....))).)))..)).))))))..............-------............ ( -20.10)
>consensus
UCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAACGGAUGUUUAGCAUUCUGGUAAUAGUACUAUGGGGAGUAAAUAAAAUAAAUA
.............(((((((.((....((.(((...(((((....)))))....))).))....)).)))))))............................... (-18.30 = -18.78 +   0.48)

alignment

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secondary structure

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Window 4

Location 7,868,957 – 7,869,068
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -35.26
Consensus MFE -27.14
Energy contribution -27.34
Covariance contribution 0.20
Combinations/Pair 1.15
Mean z-score -1.73
Structure conservation index 0.77
SVM decision value 0.43
SVM RNA-class probability 0.732823
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7868957 111 - 20766785
UGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAACGGAUGUUUAGCAUUCUG
(((((((..(((((....))....(((((((....))))))))))..))....)))))(.(((((.....(((...(((((....)))))....)))..))))))...... ( -38.30)
>DroSim_CAF1 11623 111 - 1
CGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAAUGGAUGUUUAGCAUUCUG
.((((((..(((((....))....(((((((....))))))))))..))....))))(((.((....((.(((...(((((....)))))....))).))....)).))). ( -39.00)
>DroEre_CAF1 13017 111 - 1
UGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGUAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAAUGGGUGUUUCGCAUUCUG
(((((.(..(((((....))....(((((((....))))))))))..).....)))))....(((((((..((...(((((....)))))....)))))))))........ ( -36.80)
>DroYak_CAF1 11902 111 - 1
UGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCUGAUGGUAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAACGGAUGUUUCGCAUUCUG
(((((.....((((.........((((((((....)))))))).)))).....)))))....(((((((((.....(((((....)))))....)))))))))........ ( -36.40)
>DroAna_CAF1 11253 111 - 1
CGGAAGCUGGCCGUAAUCCCGAAAUAUACGAAAAUCAGAAUCAGAGGGCAGGAUUCCUGAUUGAAAAAUCUCUUCGGCCAUUGUGGUGCCAAACGGAUGUUUAGCAUUCUG
(((((((((((((((((.(((((.........((((((((((.........)))).))))))..........)))))..)))))))).((....)).....)))).))))) ( -25.81)
>consensus
UGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCAUUGUGGUGGCAAACGGAUGUUUAGCAUUCUG
.((((.(((.((((..........(((((((....)))))))..)))))))..))))(((.((....((.(((...(((((....)))))....))).))....)).))). (-27.14 = -27.34 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,868,988 – 7,869,108
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.94
Mean single sequence MFE -40.12
Consensus MFE -31.29
Energy contribution -31.10
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -2.12
Structure conservation index 0.78
SVM decision value 0.60
SVM RNA-class probability 0.794790
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7868988 120 + 20766785
UGGCCGAGGAAAUAUUUCAGUCUGGCAUUUUGCCAUCCGAUACGGAUUUCCGUAUCUUUCGCGACUACGGACAACUGCCAGGUGAGUUGGUCACGCGAAUGCUUCAUUGGCUUGUGUAUU
.((((((.(((........(..((((.....))))..)(((((((....))))))).((((((.(....).(((((........)))))....))))))...))).))))))........ ( -39.20)
>DroSim_CAF1 11654 120 + 1
UGGCCGAGGAAAUAUUUCAGUCUGGCAUUUUGCCAUCCGAUACGGAUUUCCGUAUCUUUCGCGACUACGGACAACUGCCGGGUGAGUUGGUCACGCGAAUGCUUCAUUCGCUUGUGUACU
(((((((........((((.(((((((..((((.....(((((((....)))))))....))))(....).....)))))))))))))))))).(((((((...)))))))......... ( -39.50)
>DroEre_CAF1 13048 119 + 1
UGGCCGAGGAAAUAUUUCAGUCUGGCAUUUUACCAUCCGAUACGGAUUUCCGUAUCUUUCGCGACUACGGACAACUGCCAGGUGAGUUGGUCACGCGAGUGCCUUACUGGUUUGGU-AUU
..((((((........(((((..(((((..........(((((((....)))))))..(((((.(....).(((((........)))))....))))))))))..)))))))))))-... ( -39.80)
>DroYak_CAF1 11933 120 + 1
UGGCCGAGGAAAUAUUUCAGUCUGGCAUUUUACCAUCAGAUACGGAUUUCCGUAUCUUUCGCGACUACGGACAACUGCCAGGUGAGUUGGUCACGCGAAUGCCUUUCUGCUUUCCUCAUU
.....(((((((.....(((...((((..........((((((((....))))))))((((((.(....).(((((........)))))....))))))))))...))).)))))))... ( -42.00)
>consensus
UGGCCGAGGAAAUAUUUCAGUCUGGCAUUUUACCAUCCGAUACGGAUUUCCGUAUCUUUCGCGACUACGGACAACUGCCAGGUGAGUUGGUCACGCGAAUGCCUCACUGGCUUGUGUAUU
..(((((.(((....)))..)).))).....((((...(((((((....))))))).((((((...((.(((.(((....)))..))).))..))))))........))))......... (-31.29 = -31.10 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,868,988 – 7,869,108
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.94
Mean single sequence MFE -38.00
Consensus MFE -29.98
Energy contribution -30.22
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -2.54
Structure conservation index 0.79
SVM decision value 1.04
SVM RNA-class probability 0.904562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7868988 120 - 20766785
AAUACACAAGCCAAUGAAGCAUUCGCGUGACCAACUCACCUGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCA
.........(((...((((..(((..((((.....))))((((((((..(((((....))....(((((((....))))))))))..))....))))))...)))...))))...))).. ( -37.40)
>DroSim_CAF1 11654 120 - 1
AGUACACAAGCGAAUGAAGCAUUCGCGUGACCAACUCACCCGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCA
..(((....(((((((...)))))))(.(((.((((........)))))))))))((((.(((((((((((....)))))))(..((((.....))))..).......))))..)))).. ( -38.10)
>DroEre_CAF1 13048 119 - 1
AAU-ACCAAACCAGUAAGGCACUCGCGUGACCAACUCACCUGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGUAAAAUGCCAGACUGAAAUAUUUCCUCGGCCA
...-.......((((..(((((....))).)).......((((((.(..(((((....))....(((((((....))))))))))..).....))))))))))................. ( -34.70)
>DroYak_CAF1 11933 120 - 1
AAUGAGGAAAGCAGAAAGGCAUUCGCGUGACCAACUCACCUGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCUGAUGGUAAAAUGCCAGACUGAAAUAUUUCCUCGGCCA
..((((((((.(((...((((((((((..(((((((........)))))...))...))))))((((((((....))))))))..........))))...))).....)))))))).... ( -41.80)
>consensus
AAUAAACAAACCAAUAAAGCAUUCGCGUGACCAACUCACCUGGCAGUUGUCCGUAGUCGCGAAAGAUACGGAAAUCCGUAUCGGAUGGCAAAAUGCCAGACUGAAAUAUUUCCUCGGCCA
.................(((....(((.(((.((((........))))))))))((((......(((((((....)))))))...((((.....))))))))..............))). (-29.98 = -30.22 +   0.25)

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 10:21:22 2006