Locus 3968

Sequence ID 3L_DroMel_CAF1
Location 11,515,395 – 11,515,510
Length 115
Max. P 0.985804
window6181 window6182 window6183

overview

Window 1

Location 11,515,395 – 11,515,490
Length 95
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 76.34
Mean single sequence MFE -20.74
Consensus MFE -10.86
Energy contribution -13.14
Covariance contribution 2.28
Combinations/Pair 1.15
Mean z-score -1.78
Structure conservation index 0.52
SVM decision value 0.14
SVM RNA-class probability 0.603460
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11515395 95 + 23771897
AUCUGUAUUUUUGUUUCCAGUUUUUGAGAUAUGCUAAUAA---GCA---GUAAGAAACAUGCUAUACGAAAUUAUCCCA-AAUGGGGUAAUUAAUAACACGG
..((((....((((...((((((((......((((....)---)))---...)))))).))....))))(((((((((.-...)))))))))......)))) ( -20.50)
>DroSec_CAF1 21204 82 + 1
-------------------GUUUUUGAGAUAUGCUAAUUGUUAGCAGAGGUUAGAAACGUGCUAUACGAAAUUAUCCCA-AAUGGGGUAAUUAAUAACACGG
-------------------((((((((..(.(((((.....))))).)..))))))))(((.(((....(((((((((.-...))))))))).))).))).. ( -23.80)
>DroSim_CAF1 19871 101 + 1
AUCUGUAUUUUUGAUUCCAGUUUUUGAGUUAUGCUAAUUAUUGGCAGUGGCUAGAAACGUGCUAUACGAAAUUAUCCCA-AAUGGGGUAAUUAAUAACACGG
................((.((((((.((((((((((.....))))).)))))))))))(((.(((....(((((((((.-...))))))))).))).))))) ( -25.60)
>DroEre_CAF1 15750 102 + 1
AUCUGAAUUUUUGAUUCCAGUUUAUCAGAUAUGCUAAUCGAUAGCAGUGGCUAGAAACGUGCUAUAAGAAAUUAUCCAAAAAUGAGGUGAUUAAUAACAUGG
((((((....(((....)))....)))))).(((((.....)))))(((((.........)))))....(((((((((....)).))))))).......... ( -18.10)
>DroYak_CAF1 20044 89 + 1
--GUAUAUUUUUAGUUCCAGUUUUUUAGAUAUGCUAAUA----------AUUGGAAACGUGCCAUAAGAAAUUAUCCAA-AAUGAGGUAAUUAAUAACACGG
--............((((((((..((((.....)))).)----------))))))).((((........((((((((..-...).))))))).....)))). ( -15.72)
>consensus
AUCUGUAUUUUUGAUUCCAGUUUUUGAGAUAUGCUAAUAA_U_GCAG_GGUUAGAAACGUGCUAUACGAAAUUAUCCCA_AAUGGGGUAAUUAAUAACACGG
...................((((((......(((((.....)))))......))))))(((.(((....(((((((((.....))))))))).))).))).. (-10.86 = -13.14 +   2.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,515,395 – 11,515,490
Length 95
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 76.34
Mean single sequence MFE -17.60
Consensus MFE -11.10
Energy contribution -11.38
Covariance contribution 0.28
Combinations/Pair 1.19
Mean z-score -2.29
Structure conservation index 0.63
SVM decision value 2.02
SVM RNA-class probability 0.985804
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11515395 95 - 23771897
CCGUGUUAUUAAUUACCCCAUU-UGGGAUAAUUUCGUAUAGCAUGUUUCUUAC---UGC---UUAUUAGCAUAUCUCAAAAACUGGAAACAAAAAUACAGAU
.((((((((.(((((.(((...-.))).)))))....))))))))........---(((---(....)))).((((.......((....)).......)))) ( -19.84)
>DroSec_CAF1 21204 82 - 1
CCGUGUUAUUAAUUACCCCAUU-UGGGAUAAUUUCGUAUAGCACGUUUCUAACCUCUGCUAACAAUUAGCAUAUCUCAAAAAC-------------------
.((((((((.(((((.(((...-.))).)))))....))))))))...........(((((.....)))))............------------------- ( -19.50)
>DroSim_CAF1 19871 101 - 1
CCGUGUUAUUAAUUACCCCAUU-UGGGAUAAUUUCGUAUAGCACGUUUCUAGCCACUGCCAAUAAUUAGCAUAACUCAAAAACUGGAAUCAAAAAUACAGAU
.((((((((.(((((.(((...-.))).)))))....)))))))).((((((....(((.........)))...........)))))).............. ( -17.96)
>DroEre_CAF1 15750 102 - 1
CCAUGUUAUUAAUCACCUCAUUUUUGGAUAAUUUCUUAUAGCACGUUUCUAGCCACUGCUAUCGAUUAGCAUAUCUGAUAAACUGGAAUCAAAAAUUCAGAU
..((((...(((((.((........))..........((((((.((........)))))))).)))))))))((((((.....((....)).....)))))) ( -15.50)
>DroYak_CAF1 20044 89 - 1
CCGUGUUAUUAAUUACCUCAUU-UUGGAUAAUUUCUUAUGGCACGUUUCCAAU----------UAUUAGCAUAUCUAAAAAACUGGAACUAAAAAUAUAC--
.((((((((.(((((((.....-..)).)))))....)))))))).(((((..----------..((((.....)))).....)))))............-- ( -15.20)
>consensus
CCGUGUUAUUAAUUACCCCAUU_UGGGAUAAUUUCGUAUAGCACGUUUCUAACC_CUGC_A_CAAUUAGCAUAUCUCAAAAACUGGAAUCAAAAAUACAGAU
.((((((((.(((((.(((.....))).)))))....))))))))......................................................... (-11.10 = -11.38 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,515,420 – 11,515,510
Length 90
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 84.13
Mean single sequence MFE -17.32
Consensus MFE -12.84
Energy contribution -13.16
Covariance contribution 0.32
Combinations/Pair 1.17
Mean z-score -1.58
Structure conservation index 0.74
SVM decision value 0.04
SVM RNA-class probability 0.555801
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11515420 90 - 23771897
UGCGUCAAUCAGAUUGUUUGCCGUGUUAUUAAUUACCCCAUU-UGGGAUAAUUUCGUAUAGCAUGUUUCUUAC---UGC---UUAUUAGCAUAUCUC
.(((.((((...))))..)))((((((((.(((((.(((...-.))).)))))....))))))))........---(((---(....))))...... ( -18.40)
>DroSec_CAF1 21210 96 - 1
UGCGUCAAUCACAUUGUUCGCCGUGUUAUUAAUUACCCCAUU-UGGGAUAAUUUCGUAUAGCACGUUUCUAACCUCUGCUAACAAUUAGCAUAUCUC
.(((.((((...))))..)))((((((((.(((((.(((...-.))).)))))....))))))))...........(((((.....)))))...... ( -22.80)
>DroSim_CAF1 19896 96 - 1
UGCGUCAAUCACAUUGUUCGCCGUGUUAUUAAUUACCCCAUU-UGGGAUAAUUUCGUAUAGCACGUUUCUAGCCACUGCCAAUAAUUAGCAUAACUC
.(((.((((...))))..)))((((((((.(((((.(((...-.))).)))))....))))))))...........(((.........)))...... ( -19.30)
>DroEre_CAF1 15775 97 - 1
UGCGUCAAUCAUAUUGUUCCCCAUGUUAUUAAUCACCUCAUUUUUGGAUAAUUUCUUAUAGCACGUUUCUAGCCACUGCUAUCGAUUAGCAUAUCUG
(((...((((..(((((((...(((.............)))....))))))).....((((((.((........)))))))).)))).)))...... ( -11.42)
>DroYak_CAF1 20067 86 - 1
UGCGUCAAUCACAUUGUUCGCCGUGUUAUUAAUUACCUCAUU-UUGGAUAAUUUCUUAUGGCACGUUUCCAAU----------UAUUAGCAUAUCUA
.(((.((((...))))..)))((((((((.(((((((.....-..)).)))))....))))))))........----------.............. ( -14.70)
>consensus
UGCGUCAAUCACAUUGUUCGCCGUGUUAUUAAUUACCCCAUU_UGGGAUAAUUUCGUAUAGCACGUUUCUAACC_CUGC_A_CAAUUAGCAUAUCUC
.(((.((((...))))..)))((((((((.(((((.(((.....))).)))))....))))))))................................ (-12.84 = -13.16 +   0.32)

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 11:11:17 2006