Locus 2314

Sequence ID 2L_DroMel_CAF1
Location 6,283,731 – 6,283,856
Length 125
Max. P 0.929714
window3722 window3723 window3724

overview

Window 2

Location 6,283,731 – 6,283,830
Length 99
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.21
Mean single sequence MFE -32.08
Consensus MFE -15.86
Energy contribution -16.70
Covariance contribution 0.84
Combinations/Pair 1.14
Mean z-score -1.98
Structure conservation index 0.49
SVM decision value 0.13
SVM RNA-class probability 0.597575
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6283731 99 + 22407834
AAGA------CUGGGAGUCGUGCUUACGCAGUCUGCAGCUUCUGUUUGCCUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUAUUUGGCCUGGC---UAUUUGCCAUU
.(((------(((.(((.....)))...))))))...(((..(((((((((((........)))-)))))))).)))..--((((....))))((((---.....)))).. ( -35.80)
>DroPse_CAF1 214054 100 + 1
CAGGUCUUCUCUGGG----GUCUUCUCGCCGUC------UGCUGUUUGCCUUUCAAUUACCGGCAGGCAAACAUUGCCUUUUGCUAUUUG-CUUGGCGGGUAUUUAAAUUU
.((..((......))----..)).(((((((..------.(((((((((((.((.......)).)))))))))..((.....)).....)-).)))))))........... ( -28.60)
>DroSec_CAF1 120029 99 + 1
AAGA------CUGGGAGUCGUGCUUACGCAGUCUGCAGCUUCUGUUUGCCUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUAUUUGGCCUGGC---UAUUUGCCUUU
.(((------(((.(((.....)))...))))))...(((..(((((((((((........)))-)))))))).)))..--((((....)))).(((---.....)))... ( -34.70)
>DroSim_CAF1 134722 99 + 1
AAGA------CUGGGAGUCGUGCUUACGCAGUCUGCAGCUUCUGUUUGUCUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUAUUUGGCCUGGC---UAUUUGCAUUU
.(((------(((.(((.....)))...))))))((((((..((((((.((..((.....))..-)))))))).)))((--(((((.......))))---))).))).... ( -31.60)
>DroEre_CAF1 119713 98 + 1
AAGA------CUGGGAGUCGUGCUUACGCAGUCUGCAGCUUCUGUUUGCUUUUCAAUUACCGGG-GGCAAACACUGCAU--GGCUGUUU-GCCUGGC---UAUUUGCCUUU
.(((------(((.(((.....)))...))))))((((....(((((((((((........)))-))))))))))))..--(((.....-))).(((---.....)))... ( -32.60)
>DroPer_CAF1 213341 106 + 1
CAGGUCUUCUCUGGG----GUCUUCUCGCCGUCUACUGCUGCUGUUUGCCUUUCAAUUACCGGCAGGCAAACAUUGCCUUUUGCUAUUUG-CUUGGCGGGUAUUUAAAUUU
.((..((......))----..)).(((((((......((...(((((((((.((.......)).)))))))))..)).....((.....)-).)))))))........... ( -29.20)
>consensus
AAGA______CUGGGAGUCGUGCUUACGCAGUCUGCAGCUUCUGUUUGCCUUUCAAUUACCGGG_GGCAAACACGGCAU__GGCUAUUUGGCCUGGC___UAUUUGCAUUU
..........(..((....(((....))).(((....((...((((((((.(((.......))).))))))))..))....))).......))..)............... (-15.86 = -16.70 +   0.84)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,283,756 – 6,283,856
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.53
Mean single sequence MFE -37.48
Consensus MFE -25.57
Energy contribution -27.10
Covariance contribution 1.53
Combinations/Pair 1.10
Mean z-score -3.96
Structure conservation index 0.68
SVM decision value 1.20
SVM RNA-class probability 0.929714
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6283756 100 + 22407834
UCUGCAGCUUCUGUUUGCCUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUAUUUGGCCUGGC---UAUUUGCCAUUAAGCA------------GCCUCGUUCCUUUGAGGCUGC--
......(((..(((((((((((........)))-)))))))).)))..--((((....))))((((---.....))))....(((------------((((((......)))))))))-- ( -42.80)
>DroSec_CAF1 120054 96 + 1
UCUGCAGCUUCUGUUUGCCUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUAUUUGGCCUGGC---UAUUUGCCUUUAAGCA------------GCCU----CCUUUGAGGCUGC--
...(((((((((((((((((((........)))-)))))))).(((..--((((....)))).(((---.....)))........------------))).----.....))))))))-- ( -39.90)
>DroSim_CAF1 134747 96 + 1
UCUGCAGCUUCUGUUUGUCUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUAUUUGGCCUGGC---UAUUUGCAUUUAAGCA------------GCCU----CCUUUGAGGCUGC--
..(((((((..((((((.((..((.....))..-)))))))).)))((--(((((.......))))---))).)))).....(((------------((((----(....))))))))-- ( -37.30)
>DroEre_CAF1 119738 95 + 1
UCUGCAGCUUCUGUUUGCUUUUCAAUUACCGGG-GGCAAACACUGCAU--GGCUGUUU-GCCUGGC---UAUUUGCCUUUAACCA------------GCCU----CCUUUGAGGCUGC--
...(((((((((((((((((((........)))-))))))))......--(((((.((-(...(((---.....)))..))).))------------))).----.....))))))))-- ( -36.20)
>DroYak_CAF1 133135 96 + 1
UCUGCAGCUUCUGUUUGCUUUUCAAUUACUGGG-GGCAAACACGGCAU--GGCUCUUUGGCCUGGC---UAUUUGCCUUUAAACA------------GCCU----CCUUUGAGGCUGC--
...(((((((((((((((.(..((.....))..-)))))))).(((..--((((....)))).(((---.....)))........------------))).----.....))))))))-- ( -37.40)
>DroPer_CAF1 213368 115 + 1
UCUACUGCUGCUGUUUGCCUUUCAAUUACCGGCAGGCAAACAUUGCCUUUUGCUAUUUG-CUUGGCGGGUAUUUAAAUUUAACUACGCGGCCACUGCGCCU----CCUUUGUGCCUGCUG
......((((((((((((((.((.......)).))))))))).(((((...((((....-..)))))))))...............)))))....((((..----.....))))...... ( -31.30)
>consensus
UCUGCAGCUUCUGUUUGCCUUUCAAUUACUGGG_GGCAAACACGGCAU__GGCUAUUUGGCCUGGC___UAUUUGCCUUUAAGCA____________GCCU____CCUUUGAGGCUGC__
...((((((((((((((((.(((.......))).)))))))).(((....((((....)))).(((........)))....................)))..........)))))))).. (-25.57 = -27.10 +   1.53)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,283,756 – 6,283,856
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -33.01
Consensus MFE -19.27
Energy contribution -19.83
Covariance contribution 0.56
Combinations/Pair 1.19
Mean z-score -3.18
Structure conservation index 0.58
SVM decision value 0.40
SVM RNA-class probability 0.721675
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6283756 100 - 22407834
--GCAGCCUCAAAGGAACGAGGC------------UGCUUAAUGGCAAAUA---GCCAGGCCAAAUAGCC--AUGCCGUGUUUGCC-CCCAGUAAUUGAAAGGCAAACAGAAGCUGCAGA
--((((((((........)))))------------)))....((((.....---))))(((......)))--.(((.(((((((((-..(((...)))...)))))))....)).))).. ( -36.50)
>DroSec_CAF1 120054 96 - 1
--GCAGCCUCAAAGG----AGGC------------UGCUUAAAGGCAAAUA---GCCAGGCCAAAUAGCC--AUGCCGUGUUUGCC-CCCAGUAAUUGAAAGGCAAACAGAAGCUGCAGA
--((((((((....)----))))------------))).....(((.....---))).(((......)))--.(((.(((((((((-..(((...)))...)))))))....)).))).. ( -35.60)
>DroSim_CAF1 134747 96 - 1
--GCAGCCUCAAAGG----AGGC------------UGCUUAAAUGCAAAUA---GCCAGGCCAAAUAGCC--AUGCCGUGUUUGCC-CCCAGUAAUUGAAAGACAAACAGAAGCUGCAGA
--((((((((....)----))))------------)))......(((((((---(.(((((......)))--.)).).))))))).-..((((..(((.........)))..)))).... ( -28.90)
>DroEre_CAF1 119738 95 - 1
--GCAGCCUCAAAGG----AGGC------------UGGUUAAAGGCAAAUA---GCCAGGC-AAACAGCC--AUGCAGUGUUUGCC-CCCGGUAAUUGAAAAGCAAACAGAAGCUGCAGA
--.(((((((....)----))))------------))......(((.....---))).(((-.....)))--.((((((((((((.-...............))))))....)))))).. ( -33.89)
>DroYak_CAF1 133135 96 - 1
--GCAGCCUCAAAGG----AGGC------------UGUUUAAAGGCAAAUA---GCCAGGCCAAAGAGCC--AUGCCGUGUUUGCC-CCCAGUAAUUGAAAAGCAAACAGAAGCUGCAGA
--(((((.((...((----.(((------------(((((......)))))---))).(((......)))--...)).(((((((.-...............))))))))).)))))... ( -33.29)
>DroPer_CAF1 213368 115 - 1
CAGCAGGCACAAAGG----AGGCGCAGUGGCCGCGUAGUUAAAUUUAAAUACCCGCCAAG-CAAAUAGCAAAAGGCAAUGUUUGCCUGCCGGUAAUUGAAAGGCAAACAGCAGCAGUAGA
..((.(((.......----.(((......)))(.(((.(((....))).))).))))..(-(.....((.....))..(((((((((..((.....))..))))))))))).))...... ( -29.90)
>consensus
__GCAGCCUCAAAGG____AGGC____________UGCUUAAAGGCAAAUA___GCCAGGCCAAAUAGCC__AUGCCGUGUUUGCC_CCCAGUAAUUGAAAGGCAAACAGAAGCUGCAGA
..(((((.((..........(((............(((......))).......))).(((......)))........((((((((...(((...)))...)))))))))).)))))... (-19.27 = -19.83 +   0.56)

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 10:24:55 2006