Locus 7447

Sequence ID 3L_DroMel_CAF1
Location 20,003,420 – 20,003,547
Length 127
Max. P 0.899779
window12100 window12101

overview

Window 0

Location 20,003,420 – 20,003,518
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 62.84
Mean single sequence MFE -27.79
Consensus MFE -13.23
Energy contribution -12.95
Covariance contribution -0.28
Combinations/Pair 1.36
Mean z-score -1.32
Structure conservation index 0.48
SVM decision value 0.09
SVM RNA-class probability 0.578040
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20003420 98 + 23771897
GGCACCAGCACUCUACCAGGCAAACACUGGCAACACA---------UACAUAUUGGGCUAGCUUGCUGGCCAAACACUUUGAAUGGAGUGCG-------------AAUUGCAUUGGUUGA
.(((...((((((((((((.......)))).......---------.........((((((....))))))............)))))))).-------------...)))......... ( -31.20)
>DroSec_CAF1 93787 79 + 1
GGCAUCAGCAAUCGACC-------------------A---------UACAUAUAUGGCUGGCUUUCUGGCCAAACACUUUGAAUUAAGUGCG-------------AGUUGCAUUGGUUGA
.((....))..((((((-------------------(---------........((((..(....)..))))..(((((......)))))..-------------........))))))) ( -21.30)
>DroSim_CAF1 52714 79 + 1
GGCAACAGCACUCUACC-------------------A---------UACAUAUAUGGCUGGCUUUCUGGCCAAACACUUUGAAUUAAGUGCG-------------AAUUGCAUUGCUUGA
.((((..(((((...((-------------------(---------((....))))).(((((....)))))..............))))).-------------..))))......... ( -21.00)
>DroEre_CAF1 44141 116 + 1
GGCAUCGGCACUCUGGCAGCCAAACACUGGCCACACAUACGA---GUGUGUAUAUCACUGGCUUUCCAGCCAAACACUUUGAAUUGAGUGCC-AGGCAAGGAUGUAGCUGCAUUGGUAGA
.((((((((((((...((((((.....))))(((((......---)))))........(((((....))))).......))....)))))))-.......)))))..((((....)))). ( -35.11)
>DroYak_CAF1 49728 120 + 1
GGCAUCAGCACUCUGGCAGCCAAAAACUAUAAACACAUAUUAUACAUAUAUGUAUGGCUGGCUUUCCAACCAAACACUUUGAAUUGAGUGCUAAGGCAAGGUCGUAGCUGCAUUGGUGGA
..((((((((((.((((.(((.............((((((.......)))))).(((.(((....))).)))..(((((......)))))....)))...)))).)).)))..))))).. ( -29.40)
>DroAna_CAF1 48178 108 + 1
GGCUCCGGCACUUUAGCGGGAAAA---UAGACACACACAUUA---------AUACGGCUGGCUUUCUGUCCAAACACUCUGUAUUGAGUGAGAAAGUGAGGACGUAAUUGCAUUGGCUAG
((((((.((......)).)))...---...............---------.((((.((.(((((((.......(((((......)))))))))))).))..)))).........))).. ( -28.71)
>consensus
GGCAUCAGCACUCUACCAG_CAAA___U_G__ACACA_________UACAUAUAUGGCUGGCUUUCUGGCCAAACACUUUGAAUUGAGUGCG_____________AAUUGCAUUGGUUGA
.......(((.............................................((((((....))))))...(((((......)))))..................)))......... (-13.23 = -12.95 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,003,457 – 20,003,547
Length 90
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 67.45
Mean single sequence MFE -15.87
Consensus MFE -9.68
Energy contribution -9.80
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -1.49
Structure conservation index 0.61
SVM decision value 1.01
SVM RNA-class probability 0.899779
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20003457 90 - 23771897
AAUUCCCUUGACUUAACAU--C------GAAACCCAUUCAACCAAUGCAAUU------------CGCACUCCAUUCAAAGUGUUUGGCCAGCAAGCUAGCCCAAUAUGUA---
.......((((........--(------(((...((((.....))))...))------------))........)))).(((((.(((.((....)).))).)))))...--- ( -12.29)
>DroSec_CAF1 93805 77 - 1
AAUUCCCU---------AU--C----------CAUAUUCAACCAAUGCAACU------------CGCACUUAAUUCAAAGUGUUUGGCCAGAAAGCCAGCCAUAUAUGUA---
........---------..--.----------(((((...............------------.((((((......))))))(((((......)))))....)))))..--- ( -11.70)
>DroSim_CAF1 52732 77 - 1
AAUUCCCU---------AU--C----------CAUAUUCAAGCAAUGCAAUU------------CGCACUUAAUUCAAAGUGUUUGGCCAGAAAGCCAGCCAUAUAUGUA---
........---------..--.----------(((((....((.........------------.((((((......)))))).((((......))))))...)))))..--- ( -14.20)
>DroEre_CAF1 44181 113 - 1
AAUUUCCUUAAUUCACCAUGCCCACGAGGAAGCCAAUUCUACCAAUGCAGCUACAUCCUUGCCUGGCACUCAAUUCAAAGUGUUUGGCUGGAAAGCCAGUGAUAUACACACUC
............((((..((((..(((((((((..(((.....)))...)))...))))))...))))................(((((....)))))))))........... ( -25.30)
>consensus
AAUUCCCU_________AU__C__________CAUAUUCAACCAAUGCAACU____________CGCACUCAAUUCAAAGUGUUUGGCCAGAAAGCCAGCCAUAUAUGUA___
..............................................((.................((((((......)))))).((((......))))))............. ( -9.68 =  -9.80 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:19 2006