Locus 389

Sequence ID 2L_DroMel_CAF1
Location 1,206,435 – 1,206,569
Length 134
Max. P 0.889027
window616 window617 window618

overview

Window 6

Location 1,206,435 – 1,206,536
Length 101
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.97
Mean single sequence MFE -31.83
Consensus MFE -25.82
Energy contribution -25.27
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -1.85
Structure conservation index 0.81
SVM decision value 0.27
SVM RNA-class probability 0.661875
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1206435 101 - 22407834
GCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUGUUGAUAC-------------------UGGGCACGACCUCU
((((((((((....(((.....(((...((((......)))).))))))....((((((((.......))))))))..)))))))..-------------------..)))......... ( -30.70)
>DroPse_CAF1 2574 107 - 1
GCCAUCAAUAAACGCUGACAGAGCCAA-UGGCAGAGCAGCUGAGGCCAG-AAGAGCUCAUGGCAUUACCGUGAACUAAUGUUGAUACGGGGGC----------CACCGGGCACGACCCC-
((((((((((...((((.....(((..-.)))....)))).........-...((.((((((.....)))))).))..))))))).(((....----------..))))))........- ( -31.40)
>DroSim_CAF1 2139 101 - 1
GCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUGUUGAUAC-------------------UGGGCACGACCUCU
((((((((((....(((.....(((...((((......)))).))))))....((((((((.......))))))))..)))))))..-------------------..)))......... ( -30.70)
>DroEre_CAF1 2073 101 - 1
GCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUGUUGAUAC-------------------UGGGCACGACCUCU
((((((((((....(((.....(((...((((......)))).))))))....((((((((.......))))))))..)))))))..-------------------..)))......... ( -30.70)
>DroYak_CAF1 2224 101 - 1
GCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUGUUGAUAC-------------------UGGGCACGACCUCU
((((((((((....(((.....(((...((((......)))).))))))....((((((((.......))))))))..)))))))..-------------------..)))......... ( -30.70)
>DroPer_CAF1 2572 117 - 1
GCCAUCAAUAAACGCUGACAGAGCCAA-UGGCAGAGCAGCUGAGGCCAG-AAGAGCUCAUGACAUUACCGUGAACUAAUGUUGAUACGGGGGCCACCGGGGGCCACCGGGCACGACCCC-
((((((((((...((((.....(((..-.)))....)))).........-...((.(((((.......))))).))..))))))).(((.((((......)))).))))))........- ( -36.80)
>consensus
GCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUGUUGAUAC___________________UGGGCACGACCUCU
...(((((((....(((.....(((...((((......)))).))))))....((((((((.......))))))))..)))))))......................(((.....))).. (-25.82 = -25.27 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,206,456 – 1,206,569
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.10
Mean single sequence MFE -26.87
Consensus MFE -24.55
Energy contribution -24.63
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.60
Structure conservation index 0.91
SVM decision value 0.95
SVM RNA-class probability 0.889027
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1206456 113 + 22407834
CAUUAGUUCACGGUAAUGUCGUGAACUUUUCCUGGCCUCAGCUGUUUGGCUGCUCGGCUUUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUU-UUCAAUUUAUUUUAUUUU--CCU----
....(((((((((.....)))))))))......((.....((((...((((....))))....))))((..(((((.(((((....))))).-.)))))..))........--)).---- ( -26.60)
>DroPse_CAF1 2603 118 + 1
CAUUAGUUCACGGUAAUGCCAUGAGCUCUU-CUGGCCUCAGCUGCUCUGCCA-UUGGCUCUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUUUUUCAAUUUAUUUUGUCUUUUUUGCCUU
...........((((((((((((((..(..-..)..))).(((((...(((.-..)))...).))))........)))))).(((((((...........)))))))......))))).. ( -28.00)
>DroSim_CAF1 2160 113 + 1
CAUUAGUUCACGGUAAUGUCGUGAACUUUUCCUGGCCUCAGCUGUUUGGCUGCUCGGCUUUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUU-UUCAAUUUAUUUUAUUUU--CCG----
....(((((((((.....)))))))))......((.....((((...((((....))))....))))((..(((((.(((((....))))).-.)))))..))........--)).---- ( -27.10)
>DroEre_CAF1 2094 113 + 1
CAUUAGUUCACGGUAAUGUCGUGAACUUUUCCUGGCCUCAGCUGUUUGGCUGCUCGGCUUUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUU-UUCAAUUUAUUUUAUUUU--CCG----
....(((((((((.....)))))))))......((.....((((...((((....))))....))))((..(((((.(((((....))))).-.)))))..))........--)).---- ( -27.10)
>DroYak_CAF1 2245 113 + 1
CAUUAGUUCACGGUAAUGUCGUGAACUUUUCCUGGCCUCAGCUGUUUGGCUGCUCGGCUUUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUU-UUCAAUUUAUUUUAUUUU--CCG----
....(((((((((.....)))))))))......((.....((((...((((....))))....))))((..(((((.(((((....))))).-.)))))..))........--)).---- ( -27.10)
>DroPer_CAF1 2611 117 + 1
CAUUAGUUCACGGUAAUGUCAUGAGCUCUU-CUGGCCUCAGCUGCUCUGCCA-UUGGCUCUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUUUUUCAAUUUAUUUUGUCUUUUUUGCCU-
...........((((((((((((((..(..-..)..))).(((((...(((.-..)))...).))))........)))))).(((((((...........)))))))......))))).- ( -25.30)
>consensus
CAUUAGUUCACGGUAAUGUCGUGAACUUUUCCUGGCCUCAGCUGUUUGGCUGCUCGGCUUUGUCAGCGUUUAUUGAUGGCAUCAAAGUGUUU_UUCAAUUUAUUUUAUUUU__CCG____
....(((((((((.....))))))))).............((((...((((....))))....))))((..(((((.(((((....)))))...)))))..))................. (-24.55 = -24.63 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,206,456 – 1,206,569
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.10
Mean single sequence MFE -22.90
Consensus MFE -19.86
Energy contribution -19.53
Covariance contribution -0.33
Combinations/Pair 1.17
Mean z-score -1.65
Structure conservation index 0.87
SVM decision value 0.41
SVM RNA-class probability 0.725334
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1206456 113 - 22407834
----AGG--AAAAUAAAAUAAAUUGAA-AAACACUUUGAUGCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUG
----...--............((..((-......))..)).((.(((........)))....(((...((((......)))).)))..))...((((((((.......)))))))).... ( -22.90)
>DroPse_CAF1 2603 118 - 1
AAGGCAAAAAAGACAAAAUAAAUUGAAAAAACACUUUGAUGCCAUCAAUAAACGCUGACAGAGCCAA-UGGCAGAGCAGCUGAGGCCAG-AAGAGCUCAUGGCAUUACCGUGAACUAAUG
...............................(((..(((((((((.................(((..-.))).((((..(((....)))-....)))))))))))))..)))........ ( -25.70)
>DroSim_CAF1 2160 113 - 1
----CGG--AAAAUAAAAUAAAUUGAA-AAACACUUUGAUGCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUG
----...--............((..((-......))..)).((.(((........)))....(((...((((......)))).)))..))...((((((((.......)))))))).... ( -22.90)
>DroEre_CAF1 2094 113 - 1
----CGG--AAAAUAAAAUAAAUUGAA-AAACACUUUGAUGCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUG
----...--............((..((-......))..)).((.(((........)))....(((...((((......)))).)))..))...((((((((.......)))))))).... ( -22.90)
>DroYak_CAF1 2245 113 - 1
----CGG--AAAAUAAAAUAAAUUGAA-AAACACUUUGAUGCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUG
----...--............((..((-......))..)).((.(((........)))....(((...((((......)))).)))..))...((((((((.......)))))))).... ( -22.90)
>DroPer_CAF1 2611 117 - 1
-AGGCAAAAAAGACAAAAUAAAUUGAAAAAACACUUUGAUGCCAUCAAUAAACGCUGACAGAGCCAA-UGGCAGAGCAGCUGAGGCCAG-AAGAGCUCAUGACAUUACCGUGAACUAAUG
-..((........(((......)))........((((...(((.(((......((((.....(((..-.)))....))))))))))..)-))).))(((((.......)))))....... ( -20.10)
>consensus
____CGG__AAAAUAAAAUAAAUUGAA_AAACACUUUGAUGCCAUCAAUAAACGCUGACAAAGCCGAGCAGCCAAACAGCUGAGGCCAGGAAAAGUUCACGACAUUACCGUGAACUAAUG
........................................(((..........(((.....)))....((((......)))).))).......((((((((.......)))))))).... (-19.86 = -19.53 +  -0.33)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:45 2006