Locus 3483

Sequence ID 3L_DroMel_CAF1
Location 10,229,742 – 10,229,864
Length 122
Max. P 0.873905
window5439 window5440

overview

Window 9

Location 10,229,742 – 10,229,835
Length 93
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 80.74
Mean single sequence MFE -19.28
Consensus MFE -15.02
Energy contribution -14.80
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.90
Structure conservation index 0.78
SVM decision value 0.88
SVM RNA-class probability 0.873905
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10229742 93 - 23771897
CGCG-------CUGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAUUUGCGAAAAUGUUGG-------UAAAC-----
..((-------(((.....)))))....(((((((.(((((((((...)))))).....((((....))))....))).))))))).........-------.....----- ( -20.50)
>DroVir_CAF1 135726 103 - 1
UGCGCUACUUGCUUAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGUCGCUGAUUUGCGAAAAG-UACAACAA--------CAAUG
...(.(((((.........(((((((((((((...))..((((((...))))))......)))))))).)))((((......)))).)))-))).....--------..... ( -20.70)
>DroPse_CAF1 120253 100 - 1
CACUC-----GGCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAUUUGCGAAAAUCUACG-------AACAACAACG
...((-----((((.((((..(((.....))).......((((((...))))))...........)))).))))((.(((((....))))).)))-------)......... ( -19.60)
>DroWil_CAF1 172206 96 - 1
CACUC-----UCGGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAUUUGCGAAAAG-UACAGCAA--------GAA--
...((-----.(((.....(((((((((((((...))..((((((...))))))......)))))))).))))))..))(((((......-....))))--------)..-- ( -17.90)
>DroAna_CAF1 109809 102 - 1
CAUUC-----CCCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGCUGAUUUGCGAAAAUGUACAACAAAAACAAGC-----
.....-----...(.(((.(((((((((((((...))..((((((...))))))......)))))))).))).(((......)))....))).).............----- ( -17.40)
>DroPer_CAF1 120753 100 - 1
UACUC-----GGCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAUUUGCGAAAAUCUACG-------AACAACAACG
...((-----((((.((((..(((.....))).......((((((...))))))...........)))).))))((.(((((....))))).)))-------)......... ( -19.60)
>consensus
CACUC_____GCCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAUUUGCGAAAAU_UACA________A_A_CAA__
...................(((((((((((((...))..((((((...))))))......)))))))).))).(((......)))........................... (-15.02 = -14.80 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,229,762 – 10,229,864
Length 102
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 76.58
Mean single sequence MFE -19.39
Consensus MFE -12.47
Energy contribution -12.47
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.64
SVM decision value 0.52
SVM RNA-class probability 0.768972
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10229762 102 - 23771897
UCGUUUUUCGACAUACCUUUCUUCUUAUUCGCG-------CUGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAU
.........((((......((((.((((((.((-------(((.....)))))......((...))...............))))))))))....)))).......... ( -17.40)
>DroVir_CAF1 135749 105 - 1
---UCGCUCGC-AGUAUUUCUCUGCUGCUUGCGCUACUUGCUUAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGUCGCUGAU
---..((..((-((((......))))))..))((.....))(((.(.((((((((((((((...))..((((((...))))))......)))))))).)))).).))). ( -26.20)
>DroWil_CAF1 172227 96 - 1
GG-UGUGUC----UCCCCUUU---UCAUUCACUC-----UCGGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAU
((-..(((.----(((.....---..........-----..)))))).(((((((((((((...))..((((((...))))))......)))))))).)))))...... ( -15.03)
>DroMoj_CAF1 154334 105 - 1
---UCCCACGA-AGUCUUUCUGUGCUACUUGCUCGACGACAACGACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGUCGCUGAU
---........-.(((..((.(.((.....)).))).)))..(((((...(((((((((((...))..((((((...))))))......))))))))).)))))..... ( -20.70)
>DroAna_CAF1 109836 96 - 1
-----UGUCAGCAUACCUUUC---CUAUUCAUUC-----CCCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGCUGAU
-----.((((((.........---...(((....-----...)))...(((((((((((((...))..((((((...))))))......)))))))).)))..)))))) ( -20.10)
>DroPer_CAF1 120778 96 - 1
UC-UUUCUC----UACCUUUC---UUAUUUACUC-----GGCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGUUGAU
..-......----........---........((-----((((.....(((((((((((((...))..((((((...))))))......)))))))).))).)))))). ( -16.90)
>consensus
___UCUCUCG__AUACCUUUC___CUAUUCACUC_____CCCGAACAACAGCGAAAAUCGCAAAGCAAUCAAAUAAAAUUUGAAUAAAAGAUUUUUGUCUGCCGCUGAU
................................................(((((((((((((...))..((((((...))))))......)))))))).)))........ (-12.47 = -12.47 +   0.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:14 2006