Locus 4442

Sequence ID	3L_DroMel_CAF1
Location	12,947,763 – 12,948,030
Length	267
Max. P	0.999823

overview

Window 6

Location	12,947,763 – 12,947,883
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-43.20
Consensus MFE	-37.46
Energy contribution	-37.82
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-2.13
Structure conservation index	0.87
SVM decision value	2.38
SVM RNA-class probability	0.993239
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12947763 120 + 23771897
GGGAUCCAGGCGCGAAAGCCACUGACACAGCUGGAACUCGGCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAA
(((((((.(((......)))((((.....((((.....))))......))))...)))))))..((((((..((.......)).(((((((((....)))))).)))......)))))). ( -44.30)
>DroSec_CAF1 64990 120 + 1
GGGAUCCGGGCGCGAAAGCCACUGACACAGCUGGAACUCGGCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACCCAGCGCAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAA
(((((((((((......)))((((.....((((.....))))......))))..))))))))..((((((..(((.......))).(((((((....))))))).........)))))). ( -44.00)
>DroSim_CAF1 69342 120 + 1
GGGAUCCGGGCGCGAAAGCCACUGACACAGCUGGAACUCGGCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACCCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAA
(((((((((((......)))((((.....((((.....))))......))))..))))))))..((((((..((.......)).(((((((((....)))))).)))......)))))). ( -45.90)
>DroEre_CAF1 71041 116 + 1
GGGAUCCGGGCGCGAAAGCCA----CACAGCUGGAACUCGGCACCAAACAGUUUCAGAUUGCCAUGCCAUCAGCAAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAA
........(((((....))..----.....((((((((.(........)))))))))...))).((((((..((.......)).(((((((((....)))))).)))......)))))). ( -39.60)
>DroYak_CAF1 68758 120 + 1
GGGAUCCGGGCGCGAAAGCCACUGACACAGCUGGAACUCGGCACCAAACAGUUUCAGAUUGCCAGGCCAUCAGCAAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCCUCUUAAUGGCAA
((....(((..((....))..)))...(((((((((((.(........))))))))).)))))..(((((..((.......))((((((((((....)))))).)))).....))))).. ( -42.20)
>consensus
GGGAUCCGGGCGCGAAAGCCACUGACACAGCUGGAACUCGGCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAA
((((....(((......)))..........((((((((.(........)))))))))..)))).((((((..((.......))(..(((((((....)))))))..)......)))))). (-37.46 = -37.82 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	12,947,803 – 12,947,923
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-34.66
Consensus MFE	-28.44
Energy contribution	-29.04
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.82
SVM decision value	0.40
SVM RNA-class probability	0.720819
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12947803 120 + 23771897
GCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUGGGC
((.((((((((((((((....)).((((((..((.......)).(((((((((....)))))).)))......))))))..))))))))(((....)))...............)))))) ( -36.90)
>DroSec_CAF1 65030 120 + 1
GCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACCCAGCGCAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUAGGC
...((..((((((((((....)).((((((..(((.......))).(((((((....))))))).........))))))..))))))))(((....)))..................)). ( -31.40)
>DroSim_CAF1 69382 120 + 1
GCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACCCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUAGGC
...((..((((((((((....)).((((((..((.......)).(((((((((....)))))).)))......))))))..))))))))(((....)))..................)). ( -33.30)
>DroEre_CAF1 71077 120 + 1
GCACCAAACAGUUUCAGAUUGCCAUGCCAUCAGCAAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUGCAUUUAGGC
((((...((((((((...(((((((((.....)).......(((..(((((((....)))))))..)))....))))))).))))))))(((....))).........))))........ ( -37.90)
>DroYak_CAF1 68798 120 + 1
GCACCAAACAGUUUCAGAUUGCCAGGCCAUCAGCAAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCCUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCAAGAUUUGUACAUUUAGGC
...((..((((((((...((((((.((.....))......((.((((((((((....)))))).)))).))...)))))).))))))))(((....)))..................)). ( -33.80)
>consensus
GCACCAAACAGUUUCGGAUUCCCAUGCCAUCAGCGAACUCAGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUAGGC
...((..((((((((((....)).((((((..((.......))(..(((((((....)))))))..)......))))))..))))))))(((....)))..................)). (-28.44 = -29.04 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	12,947,843 – 12,947,955
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.52
Mean single sequence MFE	-34.06
Consensus MFE	-31.34
Energy contribution	-31.82
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.54
Structure conservation index	0.92
SVM decision value	4.17
SVM RNA-class probability	0.999823
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12947843 112 + 23771897
AGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUGGGCUGCUUGACU--CAAGCGUAUGUAUAUA------UAUACAA
....(((((((((....)))))).)))((((.(((((((((....(((.(((....))).)))..))))).)))).)))).(((((...--)))))((((((....)------))))).. ( -34.90)
>DroSec_CAF1 65070 110 + 1
AGCGCAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUAGGCUGCUUGACU--CAAGCGUAUGUAUA--------UAUACAC
...(..(((((((....)))))))..)((((.(((((((((....(((.(((....))).)))..))))).)))).)))).(((((...--)))))(((((....--------))))).. ( -30.40)
>DroSim_CAF1 69422 112 + 1
AGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUAGGCUGCUUGACU--CAAGCGAAUGUAUAUA------UAUACAC
....(((((((((....)))))).)))((((.(((((((((....(((.(((....))).)))..))))).)))).))))((((((...--))))))..(((((...------.))))). ( -32.90)
>DroEre_CAF1 71117 110 + 1
AGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUGCAUUUAGGCUGCUUGACA--CUAGCGUCUGUA--------UGUAUACAC
.(((..(((((((....)))))))..))).......(((((....(((.(((....))).)))..)))))((((.(((((.(((.....--..)))))))).)--------)))...... ( -32.50)
>DroYak_CAF1 68838 120 + 1
AGCGGAGCCGCAAAUCUUUGCGGUCUCCUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCAAGAUUUGUACAUUUAGGCUGCUUGACACACAAGCGUAUGUAUAUAUGGAUGUAUACAC
(((((((((((((....)))))).)))).((.(((((((((....(((.(((....))).)))..))))).)))).)))))(((((.....)))))...((((((((....)))))))). ( -39.60)
>consensus
AGCGGAGCCGCAAAUCUUUGCGGUCUCGUCUUAAUGGCAAAGAAAUUGUGAUUUAUGUCUCGAGAUUUGUACAUUUAGGCUGCUUGACU__CAAGCGUAUGUAUAUA______UAUACAC
...(..(((((((....)))))))..)((((.(((((((((....(((.(((....))).)))..))))).)))).)))).(((((.....)))))...((((((........)))))). (-31.34 = -31.82 +   0.48)

alignment

secondary structure

dotplot

Window 9

Location	12,947,843 – 12,947,955
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.52
Mean single sequence MFE	-25.25
Consensus MFE	-20.78
Energy contribution	-21.42
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.32
Structure conservation index	0.82
SVM decision value	0.03
SVM RNA-class probability	0.547749
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12947843 112 - 23771897
UUGUAUA------UAUAUACAUACGCUUG--AGUCAAGCAGCCCAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCUUUGCCAUUAAGACGAGACCGCAAAGAUUUGCGGCUCCGCU
.(((((.------...)))))...(((((--...)))))(((.............(((((.((......))......((((.......)))))))))((((((....))))))....))) ( -22.30)
>DroSec_CAF1 65070 110 - 1
GUGUAUA--------UAUACAUACGCUUG--AGUCAAGCAGCCUAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCUUUGCCAUUAAGACGAGACCGCAAAGAUUUGCGGCUGCGCU
((((((.--------.....))))))...--......((((((............(((((.((......))......((((.......)))))))))..((((....))))))))))... ( -26.90)
>DroSim_CAF1 69422 112 - 1
GUGUAUA------UAUAUACAUUCGCUUG--AGUCAAGCAGCCUAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCUUUGCCAUUAAGACGAGACCGCAAAGAUUUGCGGCUCCGCU
((((((.------...))))))..(((((--...)))))(((.............(((((.((......))......((((.......)))))))))((((((....))))))....))) ( -23.00)
>DroEre_CAF1 71117 110 - 1
GUGUAUACA--------UACAGACGCUAG--UGUCAAGCAGCCUAAAUGCACAAAUCUCGAGACAUAAAUCACAAUUUCUUUGCCAUUAAGACGAGACCGCAAAGAUUUGCGGCUCCGCU
((((((...--------....((((....--)))).((....))..))))))...(((((.((......))......((((.......)))))))))((((((....))))))....... ( -21.80)
>DroYak_CAF1 68838 120 - 1
GUGUAUACAUCCAUAUAUACAUACGCUUGUGUGUCAAGCAGCCUAAAUGUACAAAUCUUGAGACAUAAAUCACAAUUUCUUUGCCAUUAAGAGGAGACCGCAAAGAUUUGCGGCUCCGCU
(((((((......)))))))....((((((((.(((((..................))))).)))))).........((((.......))))((((.((((((....)))))))))))). ( -32.27)
>consensus
GUGUAUA______UAUAUACAUACGCUUG__AGUCAAGCAGCCUAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCUUUGCCAUUAAGACGAGACCGCAAAGAUUUGCGGCUCCGCU
.((((((........))))))...(((((.....)))))(((.............(((((.((......))......((((.......)))))))))((((((....))))))....))) (-20.78 = -21.42 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	12,947,883 – 12,947,992
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.90
Mean single sequence MFE	-18.62
Consensus MFE	-12.82
Energy contribution	-14.06
Covariance contribution	1.24
Combinations/Pair	1.05
Mean z-score	-1.64
Structure conservation index	0.69
SVM decision value	0.11
SVM RNA-class probability	0.588624
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12947883 109 - 23771897
ACAAGGAAACUAAAUCGUGUGCAUCAUCUCAAAU---AUAUUGUAUA------UAUAUACAUACGCUUG--AGUCAAGCAGCCCAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCU
...((....)).....(((.......((((....---....(((((.------...)))))...(((((--...)))))....................)))).......)))....... ( -16.84)
>DroSec_CAF1 65110 98 - 1
ACAAGGAAACUAAAUCGUGUGCAUU------------AAAGUGUAUA--------UAUACAUACGCUUG--AGUCAAGCAGCCUAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCU
...((....))...(((((((((((------------...(((((..--------..)))))..(((((--...)))))......)))))))).....)))................... ( -18.10)
>DroSim_CAF1 69462 100 - 1
ACAAGGAAACUAAAUCGUGUGCAUU------------AAAGUGUAUA------UAUAUACAUUCGCUUG--AGUCAAGCAGCCUAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCU
...((....))...(((((((((((------------..(((((((.------...))))))).(((((--...)))))......)))))))).....)))................... ( -19.40)
>DroEre_CAF1 71157 110 - 1
CCAUCAAAACUACAUCGUGUGCAACAUCUCAAAUAUUAAAGUGUAUACA--------UACAGACGCUAG--UGUCAAGCAGCCUAAAUGCACAAAUCUCGAGACAUAAAUCACAAUUUCU
................(((.......((((..........((((....)--------))).((((....--))))..(((.......))).........)))).......)))....... ( -14.94)
>DroYak_CAF1 68878 120 - 1
CCAAGGAAACUAAGUCGUGUGAAUCAUCUCAAAUAUUAAAGUGUAUACAUCCAUAUAUACAUACGCUUGUGUGUCAAGCAGCCUAAAUGUACAAAUCUUGAGACAUAAAUCACAAUUUCU
...((....))......(((((....((((((........(((((((......)))))))....(((((.....)))))..................))))))......)))))...... ( -23.80)
>consensus
ACAAGGAAACUAAAUCGUGUGCAUCAUCUCAAAU___AAAGUGUAUA______UAUAUACAUACGCUUG__AGUCAAGCAGCCUAAAUGUACAAAUCUCGAGACAUAAAUCACAAUUUCU
.........((......(((((((................(((((((........)))))))..(((((.....))))).......))))))).......)).................. (-12.82 = -14.06 +   1.24)

alignment

secondary structure

dotplot

Window 1

Location	12,947,923 – 12,948,030
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.45
Mean single sequence MFE	-20.26
Consensus MFE	-14.92
Energy contribution	-16.32
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.508698
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12947923 107 - 23771897
--ACUUCUUCAAAGUUUGCUUGCCAAACUACUUAGGUUCAACAAGGAAACUAAAUCGUGUGCAUCAUCUCAAAU---AUAUUGUAUA------UAUAUACAUACGCUUG--AGUCAAGCA
--..........(((((.((((...((((.....))))...)))).))))).....(((((((...........---....))))))------)..........(((((--...))))). ( -18.96)
>DroSec_CAF1 65150 96 - 1
--ACUUCUUCAAAGUUUGCUUGCCAAACUACUUAGGUUCAACAAGGAAACUAAAUCGUGUGCAUU------------AAAGUGUAUA--------UAUACAUACGCUUG--AGUCAAGCA
--..........(((((.((((...((((.....))))...)))).))))).....((((((((.------------...)))))))--------)........(((((--...))))). ( -21.20)
>DroSim_CAF1 69502 98 - 1
--ACUUCUUCAAAGUUUGCUUGCCAAACUACUUAGGUUCAACAAGGAAACUAAAUCGUGUGCAUU------------AAAGUGUAUA------UAUAUACAUUCGCUUG--AGUCAAGCA
--..........(((((.((((...((((.....))))...)))).))))).....((((((((.------------...)))))))------)..........(((((--...))))). ( -21.20)
>DroEre_CAF1 71197 110 - 1
UAACUCCUUCAAAGUUUGCUUGCCAAACUACUUAGGUUCACCAUCAAAACUACAUCGUGUGCAACAUCUCAAAUAUUAAAGUGUAUACA--------UACAGACGCUAG--UGUCAAGCA
................((((((.(..........((....))......(((((.(((((((..((((.............))))...))--------))).)).).)))--)).)))))) ( -15.72)
>DroYak_CAF1 68918 120 - 1
UAACUUCUUCAAAGUUUGCUUGCCAAACUACUUAGGUUCACCAAGGAAACUAAGUCGUGUGAAUCAUCUCAAAUAUUAAAGUGUAUACAUCCAUAUAUACAUACGCUUGUGUGUCAAGCA
............((((((.....)))))).....((((((((.((....)).....).)))))))...............(((((((......)))))))....(((((.....))))). ( -24.20)
>consensus
__ACUUCUUCAAAGUUUGCUUGCCAAACUACUUAGGUUCAACAAGGAAACUAAAUCGUGUGCAUCAUCUCAAAU___AAAGUGUAUA______UAUAUACAUACGCUUG__AGUCAAGCA
............(((((.((((...((((.....))))...)))).))))).............................(((((((........)))))))..(((((.....))))). (-14.92 = -16.32 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:58 2006