Locus 2077

Sequence ID 2R_DroMel_CAF1
Location 7,799,022 – 7,799,152
Length 130
Max. P 0.982215
window3440 window3441 window3442

overview

Window 0

Location 7,799,022 – 7,799,112
Length 90
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 73.28
Mean single sequence MFE -24.47
Consensus MFE -16.66
Energy contribution -16.33
Covariance contribution -0.33
Combinations/Pair 1.50
Mean z-score -1.92
Structure conservation index 0.68
SVM decision value 1.91
SVM RNA-class probability 0.982215
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7799022 90 + 20766785
CUCCGGAGAAAAGGAUAUAUGUAUAUAUAUGUGUCCUAG-----------------AUGUUUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUG
...((((....(((((((((((....))))))))))).(-----------------((....(((((.........)))))((((((...)))))).))).)))).. ( -28.10)
>DroSec_CAF1 50129 86 + 1
UUCCGGAGAAAAGGAUAUAUGUG----UAUGUGUCCUAG-----------------AUGUUUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUA
...((((....(((((((((...----.))))))))).(-----------------((....(((((.........)))))((((((...)))))).))).)))).. ( -25.40)
>DroSim_CAF1 52206 86 + 1
UUCCGGAGAAAAGGAUAUAUGUG----UAUGUGUCCUAG-----------------AUGUUUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUA
...((((....(((((((((...----.))))))))).(-----------------((....(((((.........)))))((((((...)))))).))).)))).. ( -25.40)
>DroEre_CAF1 54513 80 + 1
CUCCAGAGAAAUGGACAUAG----------AUGUCCUAG-----------------AUGCAUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUA
..((((......(((((...----------.)))))...-----------------((((.....))))........))))((((((...))))))........... ( -22.40)
>DroYak_CAF1 54061 80 + 1
CUCCAGAGGAAAGGACACGG----------AUGUCCUAG-----------------AUGUAUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCACUCGUA
.....(((...((((((...----------.)))))).(-----------------((....(((((.........)))))((((((...)))))).))).)))... ( -25.20)
>DroAna_CAF1 46831 99 + 1
UUCCUUAAGAAAGGAGGAAUAU--------CUUUUUUGGAUUUUUUUUUUAUGGCCAUGCAUCGAGUAUAGUUACAGCCAUUUGGCCAAAGGUCGCUGUCAGUCGAU
.(((...((((((((......)--------))))))))))....................(((((.((((((.((.(((....))).....)).))))).).))))) ( -20.30)
>consensus
CUCCGGAGAAAAGGAUAUAUGU________GUGUCCUAG_________________AUGUAUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUA
..((((.....(((((((............)))))))............................(((....)))..))))((((((...))))))........... (-16.66 = -16.33 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,799,022 – 7,799,112
Length 90
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 73.28
Mean single sequence MFE -20.63
Consensus MFE -10.53
Energy contribution -10.42
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.51
SVM decision value 1.23
SVM RNA-class probability 0.933457
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7799022 90 - 20766785
CACGAAUGACAGCAGCCUUUGGCUGCCCAGCUGUAUUUAUACUAGAAACAU-----------------CUAGGACACAUAUAUAUACAUAUAUCCUUUUCUCCGGAG
...........((((((...)))))).....(((((.(((((((((....)-----------------))))......)))).)))))....(((........))). ( -18.50)
>DroSec_CAF1 50129 86 - 1
UACGAAUGACAGCAGCCUUUGGCUGCCCAGCUGUAUUUAUACUAGAAACAU-----------------CUAGGACACAUA----CACAUAUAUCCUUUUCUCCGGAA
.....(((...((((((...)))))).....(((((.....(((((....)-----------------)))).....)))----)))))...(((........))). ( -19.70)
>DroSim_CAF1 52206 86 - 1
UACGAAUGACAGCAGCCUUUGGCUGCCCAGCUGUAUUUAUACUAGAAACAU-----------------CUAGGACACAUA----CACAUAUAUCCUUUUCUCCGGAA
.....(((...((((((...)))))).....(((((.....(((((....)-----------------)))).....)))----)))))...(((........))). ( -19.70)
>DroEre_CAF1 54513 80 - 1
UACGAAUGACAGCAGCCUUUGGCUGCCCAGCUGUAUUUAUACUAGAUGCAU-----------------CUAGGACAU----------CUAUGUCCAUUUCUCUGGAG
...........((((((...))))))((((.((((((((...)))))))).-----------------...(((((.----------...)))))......)))).. ( -24.90)
>DroYak_CAF1 54061 80 - 1
UACGAGUGACAGCAGCCUUUGGCUGCCCAGCUGUAUUUAUACUAGAUACAU-----------------CUAGGACAU----------CCGUGUCCUUUCCUCUGGAG
((((..((...((((((...))))))((((.((((((((...)))))))).-----------------)).)).)).----------.))))(((........))). ( -25.30)
>DroAna_CAF1 46831 99 - 1
AUCGACUGACAGCGACCUUUGGCCAAAUGGCUGUAACUAUACUCGAUGCAUGGCCAUAAAAAAAAAAUCCAAAAAAG--------AUAUUCCUCCUUUCUUAAGGAA
.(((........)))....((((((....((.(((....))).....)).)))))).....................--------.......(((((....))))). ( -15.70)
>consensus
UACGAAUGACAGCAGCCUUUGGCUGCCCAGCUGUAUUUAUACUAGAAACAU_________________CUAGGACAC________ACAUAUAUCCUUUUCUCCGGAA
........(((((((((...)))).....)))))..........................................................(((........))). (-10.53 = -10.42 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,799,049 – 7,799,152
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -29.98
Consensus MFE -18.65
Energy contribution -18.60
Covariance contribution -0.05
Combinations/Pair 1.26
Mean z-score -2.07
Structure conservation index 0.62
SVM decision value 0.45
SVM RNA-class probability 0.741011
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7799049 103 + 20766785
UAUGUGUCCUAG-----------------AUGUUUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUGUUUGAUGGCAAGUUGGAUUAAAUCUCGAUGGGGGAUAAAU
(((.(((.((((-----------------(....))))).))).)))(((((.(((((((...)))))))(((((.((....))))))).)))))......(((((.....))))).... ( -29.70)
>DroSec_CAF1 50152 103 + 1
UAUGUGUCCUAG-----------------AUGUUUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUAUUUGAUGGCAAGCUGGAUUAAAUCUCAAUGGGGGAUAAAU
(((.(((.((((-----------------(....))))).))).)))(((((.(((((((...)))))))(((((.((....))))))).)))))......(((((.....))))).... ( -31.90)
>DroSim_CAF1 52229 103 + 1
UAUGUGUCCUAG-----------------AUGUUUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUAUUUGAUGGCAAGUUGGAUUAAAUCUCAAUGGGGGAUAAAU
(((.(((.((((-----------------(....))))).))).)))(((((.(((((((...)))))))(((((.((....))))))).)))))......(((((.....))))).... ( -29.50)
>DroEre_CAF1 54533 99 + 1
---AUGUCCUAG-----------------AUGCAUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUAUUUGAUGGCAAGUCGGAUUAAAUCUCAAUGG-GGAUAAAU
---.((((((.(-----------------((....(((((.........)))))((((((...)))))).)))(((((.(((((....))))))))))............)-)))))... ( -26.80)
>DroYak_CAF1 54081 99 + 1
---AUGUCCUAG-----------------AUGUAUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCACUCGUAUUUGAUGGCAAGUCGGAUUAAAUCUCAAUGG-GGAUAAAU
---.((((((((-----------------((..((((.(((....))).(((.(((((((...)))))))((((.(((....))))))).))).))))...)))).....)-)))))... ( -27.20)
>DroAna_CAF1 46853 117 + 1
---CUUUUUUGGAUUUUUUUUUUAUGGCCAUGCAUCGAGUAUAGUUACAGCCAUUUGGCCAAAGGUCGCUGUCAGUCGAUGCUGAUUGCCAGUCGGAUUAAAUCUCAGGGGAAGAUAAAU
---.((((((((((((..(((...((((...(((((((.((((((.((.(((....))).....)).))))).).))))))).....))))...)))..))))).)))))))........ ( -34.80)
>consensus
___GUGUCCUAG_________________AUGUAUCUAGUAUAAAUACAGCUGGGCAGCCAAAGGCUGCUGUCAUUCGUAUUUGAUGGCAAGUCGGAUUAAAUCUCAAUGGGGGAUAAAU
....((((((............................(((....))).(((.(((((((...)))))))((((........)))))))......................))))))... (-18.65 = -18.60 +  -0.05)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:39 2006