Locus 5143

Sequence ID 2R_DroMel_CAF1
Location 16,735,899 – 16,736,017
Length 118
Max. P 0.962161
window8224 window8225 window8226

overview

Window 4

Location 16,735,899 – 16,735,990
Length 91
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 78.92
Mean single sequence MFE -20.10
Consensus MFE -13.48
Energy contribution -13.98
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.67
SVM decision value 1.15
SVM RNA-class probability 0.923082
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16735899 91 + 20766785
-UAUAUAUUUUUUUUUUUU---------------UGGUUUCGUGCCAAAUGCUUAACACUCAACAAAGUUGAGAGUUGAAGCAAUUUUCCGCAAGAGUAAUUAAAGC
-....(((((((.....((---------------((((.....))))))((((((((.((((((...)))))).)))).)))).........)))))))........ ( -20.60)
>DroVir_CAF1 65216 97 + 1
UUUG-----C-----UUUGGGGUCAGCCGCCUGACGAUUUCGUGCCAAACGCUUAACACUCCACAAAGUUGCGAGUUGAAGCAAUUUUACGCAAGAGUAAUUAAAGC
((((-----(-----(((((.(((((....)))))(....)...))))).((((...((((((......)).))))..))))........)))))............ ( -21.40)
>DroPse_CAF1 45150 72 + 1
-----------------------------------CGUUUGGUGGCAAAUGCUUAACACUCAACAAAGUUGAGAGUUGAAGCAAUUUUCCGCAAGAGUAAUUAAAGC
-----------------------------------......((((.(((((((((((.((((((...)))))).)))).))).)))).))))............... ( -19.70)
>DroSec_CAF1 43868 85 + 1
-UGU-----UUUU-UUUUU---------------UGGUUUCGUGCCAAAUGCUUAACACUCAACAAAGUUGAGAGUUGAAGCAAUUUUCCGCAAGAGUAAUUAAAGC
-...-----....-...((---------------((((.....))))))((((((((.((((((...)))))).)))).))))......(....)............ ( -19.60)
>DroYak_CAF1 50693 81 + 1
-UAU-----U-----UUUU---------------UGGUUUCGUGCCAAAUGCUUAACACUCAACAAAGUUGAGAGUUGAAGCAAUUUUCCGCAAGAGUAAUUAAAGC
-...-----.-----..((---------------((((.....))))))((((((((.((((((...)))))).)))).))))......(....)............ ( -19.60)
>DroPer_CAF1 44314 72 + 1
-----------------------------------CGUUUGGUGGCAAAUGCUUAACACUCAACAAAGUUGAGAGUUGAAGCAAUUUUCCGCAAGAAUAAUUAAAGC
-----------------------------------......((((.(((((((((((.((((((...)))))).)))).))).)))).))))............... ( -19.70)
>consensus
_U_U_____U_____UUUU_______________UGGUUUCGUGCCAAAUGCUUAACACUCAACAAAGUUGAGAGUUGAAGCAAUUUUCCGCAAGAGUAAUUAAAGC
.........................................(((..(((((((((((.((((((...)))))).)))).))).))))..)))............... (-13.48 = -13.98 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,735,899 – 16,735,990
Length 91
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 78.92
Mean single sequence MFE -19.72
Consensus MFE -13.62
Energy contribution -14.65
Covariance contribution 1.03
Combinations/Pair 1.05
Mean z-score -2.43
Structure conservation index 0.69
SVM decision value 1.54
SVM RNA-class probability 0.962161
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16735899 91 - 20766785
GCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUUGGCACGAAACCA---------------AAAAAAAAAAAAUAUAUA-
...........((.(((.(((...(((((.(((.((((((...)))))).))))))))))).))).)).....---------------..................- ( -19.60)
>DroVir_CAF1 65216 97 - 1
GCUUUAAUUACUCUUGCGUAAAAUUGCUUCAACUCGCAACUUUGUGGAGUGUUAAGCGUUUGGCACGAAAUCGUCAGGCGGCUGACCCCAAA-----G-----CAAA
(((((....(((((....((((.((((........)))).)))).)))))((((..((((((((........))))))))..))))...)))-----)-----)... ( -25.10)
>DroPse_CAF1 45150 72 - 1
GCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUUGCCACCAAACG-----------------------------------
((.............))((.....(((((.(((.((((((...)))))).))))))))....))........----------------------------------- ( -17.22)
>DroSec_CAF1 43868 85 - 1
GCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUUGGCACGAAACCA---------------AAAAA-AAAA-----ACA-
...........((.(((.(((...(((((.(((.((((((...)))))).))))))))))).))).)).....---------------.....-....-----...- ( -19.60)
>DroYak_CAF1 50693 81 - 1
GCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUUGGCACGAAACCA---------------AAAA-----A-----AUA-
...........((.(((.(((...(((((.(((.((((((...)))))).))))))))))).))).)).....---------------....-----.-----...- ( -19.60)
>DroPer_CAF1 44314 72 - 1
GCUUUAAUUAUUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUUGCCACCAAACG-----------------------------------
((.............))((.....(((((.(((.((((((...)))))).))))))))....))........----------------------------------- ( -17.22)
>consensus
GCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUUGGCACGAAACCA_______________AAAA_____A_____A_A_
...........((.(((.(((...(((((.(((.((((((...)))))).))))))))))).))).))....................................... (-13.62 = -14.65 +   1.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,735,917 – 16,736,017
Length 100
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 75.10
Mean single sequence MFE -25.14
Consensus MFE -13.55
Energy contribution -14.52
Covariance contribution 0.97
Combinations/Pair 1.27
Mean z-score -1.87
Structure conservation index 0.54
SVM decision value 0.81
SVM RNA-class probability 0.855385
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16735917 100 - 20766785
ACCCCCCUGUCCAAACGA-----CAGUC-CGUUGCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUU-GGCACGAAACCA-----
......(((((.....))-----)))..-...............((.(((.(((...(((((.(((.((((((...)))))).)))))))))))-.))).)).....----- ( -24.60)
>DroVir_CAF1 65235 104 - 1
AGCCCC-G-CGCAGCCCA-----CAAUCGCUGCGCUUUAAUUACUCUUGCGUAAAAUUGCUUCAACUCGCAACUUUGUGGAGUGUUAAGCGUUU-GGCACGAAAUCGUCAGG
.(((..-(-((((((...-----.....)))))((((....((((((....((((.((((........)))).)))).))))))..))))))..-)))(((....))).... ( -30.20)
>DroPse_CAF1 45150 87 - 1
-UCCCCCG----CGC------------C-GUCUGCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUU-GCCACCAAACG------
-......(----(..------------.-.(((((.............)))))....(((((.(((.((((((...)))))).))))))))...-)).........------ ( -20.32)
>DroGri_CAF1 62108 92 - 1
---AA-----CCAUUCCA-----GAGUCGCUGCGCUUUAAUUACUCUUGCGGAAAAUUGCUUCAGCUCGCAACUUUGUGGAGUGUUAAGCGUUU-GGCACGAAAUC------
---..-----........-----..((((..((((((....((((((.(((((...((((........)))).)))))))))))..)))))).)-)))........------ ( -22.30)
>DroEre_CAF1 45281 95 - 1
ACCCCCC-----GGCCGG-----CAGUC-CGUUGCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUU-GGCACGAAACCA-----
......(-----((((((-----...((-(((................)))))....(((((.(((.((((((...)))))).)))))))).))-))).))......----- ( -26.09)
>DroWil_CAF1 59127 101 - 1
ACCCCUUUU---UGCCUUCACCCCGGUA-UUUCGCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCGUUUCGGCACGAG--CA-----
.........---((((........))))-..............(((.(((.((((...((((.(((.((((((...)))))).))))))).)))).))).)))--..----- ( -27.30)
>consensus
ACCCCCC_____AGCCCA_____CAGUC_CUUCGCUUUAAUUACUCUUGCGGAAAAUUGCUUCAACUCUCAACUUUGUUGAGUGUUAAGCAUUU_GGCACGAAACCA_____
.............(((..............(((((.............)))))....(((((.(((.((((((...)))))).))))))))....))).............. (-13.55 = -14.52 +   0.97)

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 11:37:39 2006