Locus 7353

Sequence ID 3R_DroMel_CAF1
Location 19,463,358 – 19,463,487
Length 129
Max. P 0.984787
window11887 window11888 window11889

overview

Window 7

Location 19,463,358 – 19,463,451
Length 93
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 78.87
Mean single sequence MFE -33.48
Consensus MFE -24.69
Energy contribution -25.48
Covariance contribution 0.79
Combinations/Pair 1.11
Mean z-score -2.34
Structure conservation index 0.74
SVM decision value 1.99
SVM RNA-class probability 0.984787
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19463358 93 + 27905053
ACAGAUCGGGAGUUGUAGUCAAAAUGGGGG------------------------GCCGAGUUGGCUUGGAGCUUGGAGCUUCAGGCUUGGGGCUGGGCCUGUUGAUGGGGCUUCAAU
........((((((...(((((......((------------------------(((.((((((((((((((.....))))))))))...)))).))))).)))))..))))))... ( -37.50)
>DroSec_CAF1 62432 77 + 1
GCAGAUCGGGAGUUGUAGUCAAAAUGGG-G------------------------GCCGAGU-GGCUUGGAGCU--------------UGGGGCUGGGCCUGUUGAUGGGGCUUCAAU
........((((((...(((((.....(-(------------------------(((.(((-(((.....)))--------------....))).))))).)))))..))))))... ( -24.20)
>DroSim_CAF1 71487 92 + 1
GCAGAUCGGGAGUUGUAGUCAAAAUGGGGG------------------------GCCGAGU-GGCUUGGAGCUUGGAGCUUCAGGCUUGGGGCUGGGCCUGUUGAUGGGGCUUCAAU
........((((((...(((((......((------------------------(((.(((-((((((((((.....))))))))))....))).))))).)))))..))))))... ( -36.60)
>DroEre_CAF1 61864 84 + 1
GCAGAUCGGGAGUUGUAGUCAAAUUGGGG-------------------------GCCAAGU-GGCUUGGAGCUU-------GGGGCUUGGGGCUGGGUCUGUUGAUGGGGCUUCAAU
...........((((.((((..((..(((-------------------------(((....-(((((.((((..-------...)))).))))).))))).)..))..)))).)))) ( -27.90)
>DroYak_CAF1 73564 116 + 1
GCAAAUCGGGAGUUGUAGUCAAAAUGGGGGGCUAUGGAGCCAUGGAGCCAUGGAGCCAAGU-GGCUUGGAGCUUGAAGCUGGGGGCUUGGGGCUGGGUCUGUUGAUGGGGCUUCAAU
........((..(..(((((.........)))))..)..)).(((((((.(.(((((....-))))).)(((((.((((.....)))).)))))..(((....)))..))))))).. ( -41.20)
>consensus
GCAGAUCGGGAGUUGUAGUCAAAAUGGGGG________________________GCCGAGU_GGCUUGGAGCUUG_AGCU_CAGGCUUGGGGCUGGGCCUGUUGAUGGGGCUUCAAU
........((((((...(((((...(((...........................(((((....)))))(((((.((((.....)))).)))))...))).)))))..))))))... (-24.69 = -25.48 +   0.79)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,463,388 – 19,463,487
Length 99
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 77.40
Mean single sequence MFE -33.83
Consensus MFE -18.96
Energy contribution -20.35
Covariance contribution 1.39
Combinations/Pair 1.13
Mean z-score -1.72
Structure conservation index 0.56
SVM decision value 0.30
SVM RNA-class probability 0.678656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19463388 99 + 27905053
--------------GCCGAGUUGGCUUGGAGCUUGGAGCUUCAGGCUUGGGGCUGGGCCUGUUGAUGGGGCUUCAAUGGAAGCGUUUACGUCAAGCUCCAAAUCAGUUUUGCA
--------------((.((..((..((((((((((..(...(((((((......)))))))........(((((....))))).....)..))))))))))..))..)).)). ( -41.00)
>DroSec_CAF1 62461 84 + 1
--------------GCCGAGU-GGCUUGGAGCU--------------UGGGGCUGGGCCUGUUGAUGGGGCUUCAAUGAAAGCGUUUACGUCAAGCUCCAAAUCAGUUUUGCA
--------------((.((.(-(..((((((((--------------(((.(.((((((((((((.......)))))...)).)))))).)))))))))))..)).))..)). ( -30.80)
>DroSim_CAF1 71517 98 + 1
--------------GCCGAGU-GGCUUGGAGCUUGGAGCUUCAGGCUUGGGGCUGGGCCUGUUGAUGGGGCUUCAAUGGAAGCGUUUACGUCAAGCUCCAAAUCAGUUUUGCA
--------------((.((.(-(..((((((((((..(...(((((((......)))))))........(((((....))))).....)..))))))))))..)).))..)). ( -39.40)
>DroEre_CAF1 61893 91 + 1
--------------GCCAAGU-GGCUUGGAGCUU-------GGGGCUUGGGGCUGGGUCUGUUGAUGGGGCUUCAAUGGAAGCGUUUACGUCAAGCUCCAAAUCAGUUUUGCA
--------------((.((.(-(..(((((((((-------((.(...((((((..(((....)))..))))))((((....))))..).)))))))))))..)).))..)). ( -35.30)
>DroYak_CAF1 73604 112 + 1
CAUGGAGCCAUGGAGCCAAGU-GGCUUGGAGCUUGAAGCUGGGGGCUUGGGGCUGGGUCUGUUGAUGGGGCUUCAAUGGAAGCGUUUACGUCAAGCUGCAAAUCAGUUUUGCA
...(((.((.(.(((((....-))))).)(((((.((((.....)))).))))))).))).((((((..(((((....))))).....))))))...(((((.....))))). ( -40.50)
>DroAna_CAF1 82625 78 + 1
----------------------GUCUUGGAAACUGG------------GAGGCUGGGAGUGUUGAUGGGGCACCAAUGGAACAGUUAACGUCGAGCGCCAAAUCA-UUUUGCU
----------------------((((((....)...------------)))))....((((.((((..(((.((.(((..........))).).).)))..))))-...)))) ( -16.00)
>consensus
______________GCCGAGU_GGCUUGGAGCUUGG_______GGCUUGGGGCUGGGCCUGUUGAUGGGGCUUCAAUGGAAGCGUUUACGUCAAGCUCCAAAUCAGUUUUGCA
......................(..(((((((.................((((...)))).((((((..(((((....))))).....)))))))))))))..)......... (-18.96 = -20.35 +   1.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,463,388 – 19,463,487
Length 99
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 77.40
Mean single sequence MFE -25.15
Consensus MFE -12.82
Energy contribution -13.93
Covariance contribution 1.11
Combinations/Pair 1.24
Mean z-score -2.27
Structure conservation index 0.51
SVM decision value 1.02
SVM RNA-class probability 0.902215
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19463388 99 - 27905053
UGCAAAACUGAUUUGGAGCUUGACGUAAACGCUUCCAUUGAAGCCCCAUCAACAGGCCCAGCCCCAAGCCUGAAGCUCCAAGCUCCAAGCCAACUCGGC--------------
............((((((((((..((....(((((....)))))........(((((..........)))))..))..))))))))))(((.....)))-------------- ( -32.00)
>DroSec_CAF1 62461 84 - 1
UGCAAAACUGAUUUGGAGCUUGACGUAAACGCUUUCAUUGAAGCCCCAUCAACAGGCCCAGCCCCA--------------AGCUCCAAGCC-ACUCGGC--------------
............((((((((((........(((((....)))))..........(((...))).))--------------))))))))(((-....)))-------------- ( -24.60)
>DroSim_CAF1 71517 98 - 1
UGCAAAACUGAUUUGGAGCUUGACGUAAACGCUUCCAUUGAAGCCCCAUCAACAGGCCCAGCCCCAAGCCUGAAGCUCCAAGCUCCAAGCC-ACUCGGC--------------
............((((((((((..((....(((((....)))))........(((((..........)))))..))..))))))))))(((-....)))-------------- ( -32.00)
>DroEre_CAF1 61893 91 - 1
UGCAAAACUGAUUUGGAGCUUGACGUAAACGCUUCCAUUGAAGCCCCAUCAACAGACCCAGCCCCAAGCCCC-------AAGCUCCAAGCC-ACUUGGC--------------
............((((((((((........(((((....)))))................((.....))..)-------)))))))))(((-....)))-------------- ( -24.60)
>DroYak_CAF1 73604 112 - 1
UGCAAAACUGAUUUGCAGCUUGACGUAAACGCUUCCAUUGAAGCCCCAUCAACAGACCCAGCCCCAAGCCCCCAGCUUCAAGCUCCAAGCC-ACUUGGCUCCAUGGCUCCAUG
((((((.....))))))((((((.((....(((((....)))))................((.....)).....)).))))))....((((-....)))).((((....)))) ( -26.70)
>DroAna_CAF1 82625 78 - 1
AGCAAAA-UGAUUUGGCGCUCGACGUUAACUGUUCCAUUGGUGCCCCAUCAACACUCCCAGCCUC------------CCAGUUUCCAAGAC----------------------
.......-((((..((((((.((((.....)))).....))))))..))))..............------------..............---------------------- ( -11.00)
>consensus
UGCAAAACUGAUUUGGAGCUUGACGUAAACGCUUCCAUUGAAGCCCCAUCAACAGGCCCAGCCCCAAGCC_______CCAAGCUCCAAGCC_ACUCGGC______________
...........(((((((((((..(....)(((((....)))))..................................)))))))))))........................ (-12.82 = -13.93 +   1.11)

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 12:43:49 2006