Locus 7766

Sequence ID	3R_DroMel_CAF1
Location	20,810,356 – 20,810,447
Length	91
Max. P	0.871184

overview

Window 7

Location	20,810,356 – 20,810,447
Length	91
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	80.15
Mean single sequence MFE	-20.33
Consensus MFE	-9.84
Energy contribution	-10.34
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.80
Structure conservation index	0.48
SVM decision value	0.87
SVM RNA-class probability	0.871184
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20810356 91 + 27905053
GCCAAGUGCGAAAUUGCCAACUUGGCGUCGAGUAAUUAAAUAAUUAAUUG-AACCGAACAAAGGAAUUUCGCAAGUCA-AAGCCAAGAAAUGC
((((((((((....)))..))))))).(((..(((((((....)))))))-...))).....((.....(....)...-...))......... ( -19.60)
>DroPse_CAF1 19867 74 + 1
GCCAAGUGCGAAAUUGCCAACUUC---UGGCGUAAUUAAAUAAUUAAUUGGAAUCAAACAAGAGAAUUUCGCAAA---------AA-------
......(((((((((((((.....---)))).(((((((....)))))))..............)))))))))..---------..------- ( -17.30)
>DroEre_CAF1 23619 90 + 1
GCCAAGUGCGAAAUUGCCAACUUGGCGUCGAGUAAUUAAAUAAUUAAUUG-AACUGAACAAAGGAAUUUCGCAAGGCA--AGCCAAGAAAUGC
(((...((((((((((((.....))).((((.(((((....))))).)))-)............))))))))).))).--............. ( -23.80)
>DroYak_CAF1 19089 92 + 1
GCCAAGUGCGAAAUUGCCAACUUGGCGUCGAGUAAUUAAAUAAUUAAUUG-AACCGAACAAAGGAAUUUCGCAAGGCAAAAGCCAAGAAAUGC
(((...((((((((((((.....))).(((..(((((((....)))))))-...))).......))))))))).)))................ ( -25.00)
>DroAna_CAF1 20320 77 + 1
GCCAAGUGCUAAAUUGCCAGCUUC---UGGCGUAAUUAAAUAAUUAAUUG-AACCGCACAAAGGAAUUUCGCAAAGCG------AAG------
.((..((((......(((((...)---)))).(((((((....)))))))-....))))...))...(((((...)))------)).------ ( -19.00)
>DroPer_CAF1 19155 74 + 1
GCCAAGUGCGAAAUUGCCAACUUC---UGGCGUAAUUAAAUAAUUAAUUGGAAUCAAACAAGAGAAUUUCGCAAA---------AA-------
......(((((((((((((.....---)))).(((((((....)))))))..............)))))))))..---------..------- ( -17.30)
>consensus
GCCAAGUGCGAAAUUGCCAACUUC___UCGAGUAAUUAAAUAAUUAAUUG_AACCGAACAAAGGAAUUUCGCAAAGCA______AAG______
......(((((((((.((..............(((((((....)))))))............))))))))))).................... ( -9.84 = -10.34 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	20,810,356 – 20,810,447
Length	91
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	80.15
Mean single sequence MFE	-19.90
Consensus MFE	-10.58
Energy contribution	-10.52
Covariance contribution	-0.05
Combinations/Pair	1.06
Mean z-score	-2.33
Structure conservation index	0.53
SVM decision value	0.53
SVM RNA-class probability	0.773043
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20810356 91 - 27905053
GCAUUUCUUGGCUU-UGACUUGCGAAAUUCCUUUGUUCGGUU-CAAUUAAUUAUUUAAUUACUCGACGCCAAGUUGGCAAUUUCGCACUUGGC
..........(((.-.(...(((((((((.....(((.(((.-.((((((....))))))))).)))(((.....)))))))))))))..))) ( -20.40)
>DroPse_CAF1 19867 74 - 1
-------UU---------UUUGCGAAAUUCUCUUGUUUGAUUCCAAUUAAUUAUUUAAUUACGCCA---GAAGUUGGCAAUUUCGCACUUGGC
-------..---------..(((((((((...............((((((....))))))..((((---(...))))))))))))))...... ( -15.90)
>DroEre_CAF1 23619 90 - 1
GCAUUUCUUGGCU--UGCCUUGCGAAAUUCCUUUGUUCAGUU-CAAUUAAUUAUUUAAUUACUCGACGCCAAGUUGGCAAUUUCGCACUUGGC
((........)).--.(((.(((((((((.....(((.(((.-.((((((....))))))))).)))(((.....))))))))))))...))) ( -23.30)
>DroYak_CAF1 19089 92 - 1
GCAUUUCUUGGCUUUUGCCUUGCGAAAUUCCUUUGUUCGGUU-CAAUUAAUUAUUUAAUUACUCGACGCCAAGUUGGCAAUUUCGCACUUGGC
((.......(((....))).(((((((((.....(((.(((.-.((((((....))))))))).)))(((.....))))))))))))....)) ( -23.90)
>DroAna_CAF1 20320 77 - 1
------CUU------CGCUUUGCGAAAUUCCUUUGUGCGGUU-CAAUUAAUUAUUUAAUUACGCCA---GAAGCUGGCAAUUUAGCACUUGGC
------.((------(((...)))))...((...((((....-.((((((....))))))..((((---(...)))))......))))..)). ( -20.00)
>DroPer_CAF1 19155 74 - 1
-------UU---------UUUGCGAAAUUCUCUUGUUUGAUUCCAAUUAAUUAUUUAAUUACGCCA---GAAGUUGGCAAUUUCGCACUUGGC
-------..---------..(((((((((...............((((((....))))))..((((---(...))))))))))))))...... ( -15.90)
>consensus
______CUU______UGCCUUGCGAAAUUCCUUUGUUCGGUU_CAAUUAAUUAUUUAAUUACGCCA___CAAGUUGGCAAUUUCGCACUUGGC
....................(((((((((((.............((((((....))))))...............)).)))))))))...... (-10.58 = -10.52 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:12 2006