Locus 5933

Sequence ID	3R_DroMel_CAF1
Location	15,633,599 – 15,633,736
Length	137
Max. P	0.968473

overview

Window 5

Location	15,633,599 – 15,633,715
Length	116
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	82.70
Mean single sequence MFE	-30.78
Consensus MFE	-19.31
Energy contribution	-18.89
Covariance contribution	-0.41
Combinations/Pair	1.31
Mean z-score	-1.98
Structure conservation index	0.63
SVM decision value	0.04
SVM RNA-class probability	0.556031
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15633599 116 + 27905053
UAAAUGCAUUUGCAGCUGUGUUUGU-GCGGGGGGGCGUAAAUAGUACAGAGCGUGCUUAGUUGCGUUCGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCGA
....(((....)))(((((..((((-(...(.((((((((..(((((.....)))))...)))))))).)........)))))...)))))...((((((..........)))))). ( -35.50)
>DroVir_CAF1 286963 101 + 1
----UGUAUCUGCAGCUGUGUUUGU-GCG----CGCGUAAAUAGUGCAAAGCGCGCUUAGCUGCAUUUGCAAUUAAUUCACAG-------CAAAUGUUGCAAAUAAAUUAGCAGGCC
----....((((((((.((((((.(-(((----(.........))))))))))))))..((.((((((((............)-------))))))).))..........))))).. ( -32.90)
>DroPse_CAF1 172551 116 + 1
UAAAUGUAUCUGUAUCUGUAUCUGUUGUGUG-GGGCGUAAAUAGUGCAGAGUGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAA
.........((((..((((........((..-((((.((...(((((.....)))))...)))).))..))........))))...))))....((((((..........)))))). ( -25.49)
>DroMoj_CAF1 262321 108 + 1
----CAUAGCUGCAGCUGUGUUUGU-GCG----CGCGUAAAUAGCGCAAAGCGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGCAAACAGCAAAUGUUGCAAAUAAAUUAGCAGGCC
----.....((((.((((((...((-(((----(((((.....))))...))))))(((((.((....)).)))))..))))))...((((....))))...........))))... ( -35.80)
>DroAna_CAF1 154904 113 + 1
UAAAUGUAUCUGCAUCUGUGUUUGU-GCGG---GGCGUAAAUAGUGCAGAGCGUGCUUAGUUGCGUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAA
....(((.(((((((...(((((((-((..---.))))))))))))))))..(((.((((((((....))))))))..)))........)))..((((((..........)))))). ( -29.70)
>DroPer_CAF1 190878 110 + 1
UAAAUGUAUCU------GUAUCUGUUGUGUG-GGGCGUAAAUAGUGCAGAGUGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAA
...........------.....((((((...-(((((((............))))))).(..((((((((...................))))))))..)..........)))))). ( -25.31)
>consensus
UAAAUGUAUCUGCAGCUGUGUUUGU_GCG____GGCGUAAAUAGUGCAGAGCGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAA
.........((((.....(((((((.((......))......(((((.....))))).....((((((((...................)))))))).))))))).....))))... (-19.31 = -18.89 +  -0.41)

alignment

secondary structure

dotplot

Window 6

Location	15,633,638 – 15,633,736
Length	98
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	79.66
Mean single sequence MFE	-22.36
Consensus MFE	-16.41
Energy contribution	-15.66
Covariance contribution	-0.75
Combinations/Pair	1.36
Mean z-score	-2.94
Structure conservation index	0.73
SVM decision value	1.63
SVM RNA-class probability	0.968473
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15633638 98 + 27905053
AUAGUACAGAGCGUGCUUAGUUGCGUUCGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCGACAAA---AAGUGUCUGCAAGUGAA
...((((.....))))((((((((....))))))))(((((.(....).(((...(((((..........)))))((((..---...)))))))..))))) ( -24.50)
>DroPse_CAF1 172590 84 + 1
AUAGUGCAGAGUGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAACAAA---AAC--------------
..(((((.....)))))..(..((((((((...................))))))))..).....................---...-------------- ( -18.51)
>DroGri_CAF1 189848 90 + 1
AUAGCGCAAAUCGCGCUUAGUUGCAUUUGCAAUUAAUGCAAUGCAAACAGCGAAUGUUGCAAAUAAAUUAGCAGGCUAAAA---AAC-------A-ACAAU
.....((((....((((...(((((((.(((.....))))))))))..))))....)))).......((((....))))..---...-------.-..... ( -23.60)
>DroMoj_CAF1 262352 92 + 1
AUAGCGCAAAGCGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGCAAACAGCAAAUGUUGCAAAUAAAUUAGCAGGCCAAAU-GCAGC-------A-ACAAC
...((((...))))(((..(..((((((((...................))))))))..)..........(((.......)-)))))-------.-..... ( -23.91)
>DroAna_CAF1 154940 99 + 1
AUAGUGCAGAGCGUGCUUAGUUGCGUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAACAAAA--AAGUAUCUGCAAGUGAA
....(((((((((((.((((((((....))))))))..))).(....).))...((((((..........))))))......--.....))))))...... ( -25.10)
>DroPer_CAF1 190911 84 + 1
AUAGUGCAGAGUGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAACAAA---AAC--------------
..(((((.....)))))..(..((((((((...................))))))))..).....................---...-------------- ( -18.51)
>consensus
AUAGUGCAGAGCGCGCUUAGUGGCAUUUGCAAUUAAUUCACAGUAAACAGCAAAUGUUGCAAAUAAAUUAGCAGCAACAAA___AAC_______A____A_
..(((((.....)))))..(..((((((((...................))))))))..)......................................... (-16.41 = -15.66 +  -0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:22 2006