Locus 573

Sequence ID 3R_DroMel_CAF1
Location 2,141,446 – 2,141,564
Length 118
Max. P 0.982527
window913 window914 window915 window916

overview

Window 3

Location 2,141,446 – 2,141,541
Length 95
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 67.69
Mean single sequence MFE -29.89
Consensus MFE -8.46
Energy contribution -11.68
Covariance contribution 3.23
Combinations/Pair 1.17
Mean z-score -2.75
Structure conservation index 0.28
SVM decision value 1.92
SVM RNA-class probability 0.982527
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2141446 95 + 27905053
ACUGUUAGGUUGCACUUAAAUUGCAGGGCCAAGGUGCACUUCGAAUAGGAAAAGACA--------UUGCAAUUUCACUUGCAAUUGCAU-UUGCAAUUGCAGGU
.(((((.((.(((((((..............)))))))..)).))))).........--------..........((((((((((((..-..)))))))))))) ( -27.84)
>DroPse_CAF1 256021 100 + 1
ACAGCUUGGA-ACAGACAAAUUGCAGAGA--AGACUGGCUACGGGUACGGCUACCCAUUGCGGCCCAUUGAUU-GCCUUGCCAUUUAUUUGUGCAAUUGCAGGU
...(((((..-.......(((((((.(((--.((.((((...(((((....))))).....(((.........-)))..)))).)).))).))))))).))))) ( -27.40)
>DroSec_CAF1 284125 94 + 1
ACUGUUGGGUUGCACUUU-AUUGCAGGGCAAAGGUGCAAUUCCAAUAGGAAAAAACA--------UAGCAAUUGCACUUGCAAUCGCAU-UUGCAAUUGCAGGU
.(((((((((((((((((-..(((...)))))))))))).)))))))).........--------..(((((((((..(((....))).-.))))))))).... ( -39.90)
>DroEre_CAF1 288137 89 + 1
ACAGUUGGGUUGCAGUUAAAUUGCAGGGCCAAGGUGCAAUUGCAAUAGGAAAAGACA--------UAGUGAUU------GCAAUUGCAA-UUGCAAUUGCAGGU
.(((((((((((((((...))))))..)))....((((((((((((...........--------.....)))------))))))))).-...))))))..... ( -26.19)
>DroYak_CAF1 289596 89 + 1
ACAGUUAGCUUGCAGUUAAAUUGCAGGGCCAAGGUGGAAUUGCAAUAGGAAAAGACA--------UAGUGAUU------GCAAUUGCAU-UUGCAAUUGCAGGU
.......((((((((((..(((((((..((.....))..)))))))...........--------..(..(.(------((....))).-)..))))))))))) ( -28.40)
>DroPer_CAF1 258384 100 + 1
ACAGCUUGGA-ACAGACAAAUUGCAGAGG--AGACUGGCUACGGGUACGGCUACCCAUUGCGGCCCAUUGAUU-GCCUUGCCAUUUCUUUGUGCAAUUGCAGGU
...(((((..-.......(((((((((((--(((.((((...(((((....))))).....(((.........-)))..))))))))))).))))))).))))) ( -29.60)
>consensus
ACAGUUAGGUUGCAGUUAAAUUGCAGGGCCAAGGUGCAAUUCCAAUAGGAAAAGACA________UAGUGAUU___CUUGCAAUUGCAU_UUGCAAUUGCAGGU
...(((((.((((((.....)))))).((....))......)))))..............................(((((((((((.....))))))))))). ( -8.46 = -11.68 +   3.23) 

alignment

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secondary structure

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Window 4

Location 2,141,446 – 2,141,541
Length 95
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 67.69
Mean single sequence MFE -24.17
Consensus MFE -8.46
Energy contribution -9.60
Covariance contribution 1.14
Combinations/Pair 1.15
Mean z-score -2.33
Structure conservation index 0.35
SVM decision value 1.57
SVM RNA-class probability 0.964382
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2141446 95 - 27905053
ACCUGCAAUUGCAA-AUGCAAUUGCAAGUGAAAUUGCAA--------UGUCUUUUCCUAUUCGAAGUGCACCUUGGCCCUGCAAUUUAAGUGCAACCUAACAGU
((.(((((((((..-..))))))))).)).((((((((.--------.(((.((((......))))........)))..))))))))................. ( -22.30)
>DroPse_CAF1 256021 100 - 1
ACCUGCAAUUGCACAAAUAAAUGGCAAGGC-AAUCAAUGGGCCGCAAUGGGUAGCCGUACCCGUAGCCAGUCU--UCUCUGCAAUUUGUCUGU-UCCAAGCUGU
((..(((((((((........((((..(((-.........)))...(((((((....))))))).))))....--....))))).))))..))-.......... ( -25.69)
>DroSec_CAF1 284125 94 - 1
ACCUGCAAUUGCAA-AUGCGAUUGCAAGUGCAAUUGCUA--------UGUUUUUUCCUAUUGGAAUUGCACCUUUGCCCUGCAAU-AAAGUGCAACCCAACAGU
....(((((((((.-.(((....)))..)))))))))..--------((((..((((....))))((((((..((((...)))).-...))))))...)))).. ( -29.80)
>DroEre_CAF1 288137 89 - 1
ACCUGCAAUUGCAA-UUGCAAUUGC------AAUCACUA--------UGUCUUUUCCUAUUGCAAUUGCACCUUGGCCCUGCAAUUUAACUGCAACCCAACUGU
...(((((((((((-(.(.((..((------(.......--------)))..)).)..))))))))))))..((((...((((.......))))..)))).... ( -21.10)
>DroYak_CAF1 289596 89 - 1
ACCUGCAAUUGCAA-AUGCAAUUGC------AAUCACUA--------UGUCUUUUCCUAUUGCAAUUCCACCUUGGCCCUGCAAUUUAACUGCAAGCUAACUGU
...(((((((((..-..))))))))------).......--------(((..((....((((((...((.....))...))))))..))..))).......... ( -19.90)
>DroPer_CAF1 258384 100 - 1
ACCUGCAAUUGCACAAAGAAAUGGCAAGGC-AAUCAAUGGGCCGCAAUGGGUAGCCGUACCCGUAGCCAGUCU--CCUCUGCAAUUUGUCUGU-UCCAAGCUGU
((..(((((((((...(((..((((..(((-.........)))...(((((((....))))))).)))).)))--....))))).))))..))-.......... ( -26.20)
>consensus
ACCUGCAAUUGCAA_AUGCAAUUGCAAG___AAUCACUA________UGUCUUUUCCUAUUCGAAGUCCACCUUGGCCCUGCAAUUUAACUGCAACCAAACUGU
...(((((((((.....))))))))).....................................................((((.......)))).......... ( -8.46 =  -9.60 +   1.14) 

alignment

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secondary structure

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dotplot

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Window 5

Location 2,141,473 – 2,141,564
Length 91
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 66.11
Mean single sequence MFE -26.85
Consensus MFE -10.28
Energy contribution -12.26
Covariance contribution 1.97
Combinations/Pair 1.11
Mean z-score -1.94
Structure conservation index 0.38
SVM decision value 0.88
SVM RNA-class probability 0.873137
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2141473 91 + 27905053
GCCAAGGUGCACUUCGAAUAGGAAAAGACA--------UUGCAAUUUCACUUGCAAUUGCAU-UUGCAAUUGCAGGUUGAAGGUGUGA--------AGAAGCCGUCAG----
.....(((...((((.....(.......).--------..(((.((((((((((((((((..-..))))))))))).))))).)))))--------))..))).....---- ( -29.30)
>DroPse_CAF1 256047 100 + 1
GA--AGACUGGCUACGGGUACGGCUACCCAUUGCGGCCCAUUGAUU-GCCUUGCCAUUUAUUUGUGCAAUUGCAGGUUGAAGGUGUAA--------A-CAGCCAUCAACAUC
..--.((.(((((..(((((....))))).(((((.((......((-((.((((((......)).))))..))))......)))))))--------.-.)))))))...... ( -28.00)
>DroSec_CAF1 284151 91 + 1
GCAAAGGUGCAAUUCCAAUAGGAAAAAACA--------UAGCAAUUGCACUUGCAAUCGCAU-UUGCAAUUGCAGGUUGAAGGUGUGA--------AGGAGCCGUCAG----
(((....)))..((((....))))......--------..(((((((((..(((....))).-.)))))))))....(((.(((....--------....))).))).---- ( -27.80)
>DroEre_CAF1 288164 85 + 1
GCCAAGGUGCAAUUGCAAUAGGAAAAGACA--------UAGUGAUU------GCAAUUGCAA-UUGCAAUUGCAGGUCGAAGGUGUGA--------AGCAGCCGUCAG----
.((....(((....)))...))....(((.--------...(((((------((((((((..-..))))))))).))))..(((....--------....))))))..---- ( -25.50)
>DroYak_CAF1 289623 93 + 1
GCCAAGGUGGAAUUGCAAUAGGAAAAGACA--------UAGUGAUU------GCAAUUGCAU-UUGCAAUUGCAGGUUGAAGGUGUGAAGGUGUAAAGCAGCUGUCAG----
.....((..(...(((..((.(.....(((--------(..(((((------((((((((..-..))))))))).))))...)))).....).))..))).)..))..---- ( -22.20)
>DroPer_CAF1 258410 100 + 1
GG--AGACUGGCUACGGGUACGGCUACCCAUUGCGGCCCAUUGAUU-GCCUUGCCAUUUCUUUGUGCAAUUGCAGGUUAAAGGUGUAA--------A-CAGCCAUCAACAUC
(.--.((.(((((..(((((....))))).(((((.((..((((((-((.((((((......)).))))..))).))))).)))))))--------.-.)))))))..)... ( -28.30)
>consensus
GCCAAGGUGCAAUUCCAAUAGGAAAAGACA________UAGUGAUU___CUUGCAAUUGCAU_UUGCAAUUGCAGGUUGAAGGUGUGA________AGCAGCCGUCAG____
.................................................(((((((((((.....)))))))))))((((.(((................))).)))).... (-10.28 = -12.26 +   1.97) 

alignment

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secondary structure

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dotplot

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Window 6

Location 2,141,473 – 2,141,564
Length 91
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 66.11
Mean single sequence MFE -22.58
Consensus MFE -7.42
Energy contribution -8.34
Covariance contribution 0.92
Combinations/Pair 1.21
Mean z-score -1.85
Structure conservation index 0.33
SVM decision value 0.23
SVM RNA-class probability 0.646276
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2141473 91 - 27905053
----CUGACGGCUUCU--------UCACACCUUCAACCUGCAAUUGCAA-AUGCAAUUGCAAGUGAAAUUGCAA--------UGUCUUUUCCUAUUCGAAGUGCACCUUGGC
----(..(.(((..((--------((............(((((((((..-..)))))))))((.((((..((..--------.))..))))))....)))).)).).)..). ( -21.60)
>DroPse_CAF1 256047 100 - 1
GAUGUUGAUGGCUG-U--------UUACACCUUCAACCUGCAAUUGCACAAAUAAAUGGCAAGGC-AAUCAAUGGGCCGCAAUGGGUAGCCGUACCCGUAGCCAGUCU--UC
((((((((.((.((-.--------...)))).))))).(((..((((.((......)))))).))-))))...((((.((.(((((((....))))))).))..))))--.. ( -28.30)
>DroSec_CAF1 284151 91 - 1
----CUGACGGCUCCU--------UCACACCUUCAACCUGCAAUUGCAA-AUGCGAUUGCAAGUGCAAUUGCUA--------UGUUUUUUCCUAUUGGAAUUGCACCUUUGC
----.(((.((.....--------.....)).)))...(((((((((..-..))))))))).((((((((.(.(--------((........))).).))))))))...... ( -24.40)
>DroEre_CAF1 288164 85 - 1
----CUGACGGCUGCU--------UCACACCUUCGACCUGCAAUUGCAA-UUGCAAUUGC------AAUCACUA--------UGUCUUUUCCUAUUGCAAUUGCACCUUGGC
----..(((((.((..--------...))))...((..(((((((((..-..))))))))------).))....--------.)))....((...(((....)))....)). ( -19.90)
>DroYak_CAF1 289623 93 - 1
----CUGACAGCUGCUUUACACCUUCACACCUUCAACCUGCAAUUGCAA-AUGCAAUUGC------AAUCACUA--------UGUCUUUUCCUAUUGCAAUUCCACCUUGGC
----..(((((.((.....)).)...............(((((((((..-..))))))))------).......--------)))).......................... ( -14.40)
>DroPer_CAF1 258410 100 - 1
GAUGUUGAUGGCUG-U--------UUACACCUUUAACCUGCAAUUGCACAAAGAAAUGGCAAGGC-AAUCAAUGGGCCGCAAUGGGUAGCCGUACCCGUAGCCAGUCU--CC
......((.(((((-.--------((((..........(((..((((.((......))))))(((-.........))))))..(((((....))))))))).))))))--). ( -26.90)
>consensus
____CUGACGGCUGCU________UCACACCUUCAACCUGCAAUUGCAA_AUGCAAUUGCAAG___AAUCACUA________UGUCUUUUCCUAUUCGAAGUCCACCUUGGC
.....(((.((..................)).)))...(((((((((.....)))))))))................................................... ( -7.42 =  -8.34 +   0.92) 

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 09:46:28 2006