Locus 3981

Sequence ID 2R_DroMel_CAF1
Location 13,139,605 – 13,139,726
Length 121
Max. P 0.777502
window6424 window6425 window6426 window6427

overview

Window 4

Location 13,139,605 – 13,139,707
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 82.27
Mean single sequence MFE -25.19
Consensus MFE -17.37
Energy contribution -18.07
Covariance contribution 0.70
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.69
SVM decision value 0.39
SVM RNA-class probability 0.717173
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13139605 102 + 20766785
-AGACAU-GACAA---AAA----AACAAAAAACACAACAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGCUGUCUAUUGUU------
-((((..-(((((---((.----..............(((((((.(((........))).)))))))(((((.....)))))....)))))))((....))))))......------ ( -24.30)
>DroPse_CAF1 33321 112 + 1
-AGACACAGACAA---GAAAAAAAAGACAAAACAAAACAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAGUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUUGCUGU-
-....((((.(((---.((......((((((((....(((((((.(((........))).)))))))(((((.....)))))...))))))))(((.....)))..)).)))))))- ( -31.50)
>DroEre_CAF1 33925 85 + 1
-AGACA-------------------------ACACAACAUUUUGCCGCACGCUUCAACGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGCUGACUAUUGUU------
-.....-------------------------....((((........((.(((....(((((((((((((((.....))))))..)))))))))...))))).....))))------ ( -18.52)
>DroYak_CAF1 34096 105 + 1
-AGACAU-GACAA---AAA-AAAAACAAAAAACAAAACAUUUUGCCCCACGCUUCAACGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGCUGACUAUUGUU------
-......-(((((---...-.....(((((.........)))))...((.(((....(((((((((((((((.....))))))..)))))))))...)))))....)))))------ ( -19.90)
>DroAna_CAF1 33440 108 + 1
GAGACA--GACAGCGGAAA-GAAAUACAGAAAUACAACAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUU------
.(((((--....((((...-(((((.............))))).)))).........(((((((((((((((.....))))))..)))))))))......)))))......------ ( -27.52)
>DroPer_CAF1 33033 112 + 1
-AGACACAGACAA---GAGAAAAA-AACAAAACAAAACAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAGUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUUGCUGUU
-............---........-((((.(((((.((((((.(((....((....))((((((((((((((.....))))))..))))))))))).))))))...)))))..)))) ( -29.40)
>consensus
_AGACA__GACAA___AAA_AAAAAAAAAAAACAAAACAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUU______
..............................((((..(((.((.(((....((....))((((((((((((((.....))))))..))))))))))).)).)))....))))...... (-17.37 = -18.07 +   0.70)

alignment

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secondary structure

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Window 5

Location 13,139,605 – 13,139,707
Length 102
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 82.27
Mean single sequence MFE -26.98
Consensus MFE -20.66
Energy contribution -20.38
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -1.51
Structure conservation index 0.77
SVM decision value 0.21
SVM RNA-class probability 0.637154
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13139605 102 - 20766785
------AACAAUAGACAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUGUUGUGUUUUUUGUU----UUU---UUGUC-AUGUCU-
------(((((.(.(((((.((.((((((..((......)).)))))).))((((((((((........))))))))))))))).)...)))))----...---.....-......- ( -26.50)
>DroPse_CAF1 33321 112 - 1
-ACAGCAACAAUAGACAUCUGGCCGACAAAACUAAGCCAAGACUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUGUUUUGUUUUGUCUUUUUUUUC---UUGUCUGUGUCU-
-...........((((((..(((.((.((((..(((.((((((....((.(((((((((((........))))))))))).)).)))))).)))..)))).---))))).))))))- ( -31.60)
>DroEre_CAF1 33925 85 - 1
------AACAAUAGUCAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGUUGAAGCGUGCGGCAAAAUGUUGUGU-------------------------UGUCU-
------.((((((((((((((((............)))).....))))))(((((((((((........)))))))))))...)))-------------------------)))..- ( -25.80)
>DroYak_CAF1 34096 105 - 1
------AACAAUAGUCAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGUUGAAGCGUGGGGCAAAAUGUUUUGUUUUUUGUUUUU-UUU---UUGUC-AUGUCU-
------.(((...(((....))).(((((((..(((.(((((.....((.(((((((((.(........).))))))))).))....))))).))).-.))---)))))-.)))..- ( -22.00)
>DroAna_CAF1 33440 108 - 1
------AACAAUAGACAUCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUGUUGUAUUUCUGUAUUUC-UUUCCGCUGUC--UGUCUC
------....(((((((.(((((............))))(((....((((.((((((((((........))))))))))))))....))).......-.....).))))--)))... ( -26.70)
>DroPer_CAF1 33033 112 - 1
AACAGCAACAAUAGACAUCUGGCCGACAAAACUAAGCCAAGACUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUGUUUUGUUUUGUU-UUUUUCUC---UUGUCUGUGUCU-
.(((((((((((((...((((((............))).)))))))))..(((((((((((........)))))))))))............-........---))).))))....- ( -29.30)
>consensus
______AACAAUAGACAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUGUUGUGUUUUUUGUUUUU_UUU___UUGUC__UGUCU_
........((((((.(...((((............)))).).))))))..(((((((((((........)))))))))))..................................... (-20.66 = -20.38 +  -0.28)

alignment

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secondary structure

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Window 6

Location 13,139,633 – 13,139,726
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.27
Mean single sequence MFE -29.30
Consensus MFE -20.28
Energy contribution -20.39
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.69
SVM decision value 0.29
SVM RNA-class probability 0.670078
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13139633 93 + 20766785
CAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGCUGUCUAUUGUU---------------------------GUUGUAAUCACAAUGGGUA
......(((....((....))((((((((((((((.....))))))..)))))))))))......((((((((.---------------------------((....)).)))))))).. ( -24.70)
>DroPse_CAF1 33354 114 + 1
CAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAGUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUUGCUGU------UGCUGUUGCCGUUGCUGUUGUAAUUACAAUGGCUA
......(((((((((..((((((((.((..((..(((.(((.((((..........))))))))))..))..))..)))------)))))..).)).))).(((((....)))))))).. ( -35.80)
>DroEre_CAF1 33936 93 + 1
CAUUUUGCCGCACGCUUCAACGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGCUGACUAUUGUU---------------------------GUUGUAAUUACAAUAGGUA
.....((((.((.(((....(((((((((((((((.....))))))..)))))))))...)))))........(---------------------------(((((....)))))))))) ( -24.80)
>DroYak_CAF1 34127 93 + 1
CAUUUUGCCCCACGCUUCAACGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGCUGACUAUUGUU---------------------------GUUGUAAUUACAAUAGCUA
..........((.(((....(((((((((((((((.....))))))..)))))))))...)))))......(((---------------------------(((((....)))))))).. ( -24.90)
>DroAna_CAF1 33474 90 + 1
CAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUU---------------------------GUUGUAAUUACAAUGG---
(((((.(((....((....))((((((((((((((.....))))))..))))))))))).))))).(((((((.---------------------------((....)).)))))))--- ( -26.80)
>DroPer_CAF1 33065 120 + 1
CAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAGUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUUGCUGUUGCUGUUGCUGUUGCCGUUGCUGUUGUAAUUACAAUGGCUA
......((.(((.((..((((((((.((..((..(((.(((.((((..........))))))))))..))..))..))))))))..))))).))....((((((((....)))))))).. ( -38.80)
>consensus
CAUUUUGCCGCACGCUUCAGCGACAAAAUGGUCAACAAUCUUGGCUUAGUUUUGUCGGCCAGAUGUCUAUUGUU___________________________GUUGUAAUUACAAUGGCUA
......(((....((....))((((((((((((((.....))))))..))))))))))).......(((((((.....................................)))))))... (-20.28 = -20.39 +   0.11)

alignment

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secondary structure

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Window 7

Location 13,139,633 – 13,139,726
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.27
Mean single sequence MFE -25.88
Consensus MFE -20.41
Energy contribution -20.13
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -2.01
Structure conservation index 0.79
SVM decision value 0.55
SVM RNA-class probability 0.777502
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13139633 93 - 20766785
UACCCAUUGUGAUUACAAC---------------------------AACAAUAGACAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUG
......((((....))))(---------------------------((((((.......((((............))))..)))))))..(((((((((((........))))))))))) ( -23.40)
>DroPse_CAF1 33354 114 - 1
UAGCCAUUGUAAUUACAACAGCAACGGCAACAGCA------ACAGCAACAAUAGACAUCUGGCCGACAAAACUAAGCCAAGACUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUG
..(((.((((..........)))).)))....((.------...))..((((((...((((((............))).)))))))))..(((((((((((........))))))))))) ( -31.90)
>DroEre_CAF1 33936 93 - 1
UACCUAUUGUAAUUACAAC---------------------------AACAAUAGUCAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGUUGAAGCGUGCGGCAAAAUG
......((((....)))).---------------------------..((((((((...((((............)))).))))))))..(((((((((((........))))))))))) ( -23.90)
>DroYak_CAF1 34127 93 - 1
UAGCUAUUGUAAUUACAAC---------------------------AACAAUAGUCAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGUUGAAGCGUGGGGCAAAAUG
......((((....)))).---------------------------..((((((((...((((............)))).))))))))..(((((((((.(........).))))))))) ( -20.00)
>DroAna_CAF1 33474 90 - 1
---CCAUUGUAAUUACAAC---------------------------AACAAUAGACAUCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUG
---...((((....))))(---------------------------((((((.......((((............))))..)))))))..(((((((((((........))))))))))) ( -23.70)
>DroPer_CAF1 33065 120 - 1
UAGCCAUUGUAAUUACAACAGCAACGGCAACAGCAACAGCAACAGCAACAAUAGACAUCUGGCCGACAAAACUAAGCCAAGACUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUG
..(((.((((....))))..(((...((..((((....((....)).......((((..(((.(((((...((......))..))))).)))...))))))))..)).))))))...... ( -32.40)
>consensus
UAGCCAUUGUAAUUACAAC___________________________AACAAUAGACAGCUGGCCGACAAAACUAAGCCAAGAUUGUUGACCAUUUUGUCGCUGAAGCGUGCGGCAAAAUG
......((((....))))..............................((((((.(...((((............)))).).))))))..(((((((((((........))))))))))) (-20.41 = -20.13 +  -0.28)

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 11:08:53 2006