Locus 560

Sequence ID	2L_DroMel_CAF1
Location	1,741,774 – 1,741,954
Length	180
Max. P	0.955205

overview

Window 7

Location	1,741,774 – 1,741,874
Length	100
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	73.18
Mean single sequence MFE	-49.80
Consensus MFE	-18.69
Energy contribution	-19.75
Covariance contribution	1.06
Combinations/Pair	1.16
Mean z-score	-3.31
Structure conservation index	0.38
SVM decision value	1.45
SVM RNA-class probability	0.955205
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1741774 100 + 22407834
CAG------------UUCCGGCGUCUGCAGCCUCAAGGGUCACCAUGGUG--ACCCCGACAGCGGUUGCCUGGGCAUCAACUGUUGCACCA---CGGCGG---CCAGCUCGGAGCUGUCC
(((------------(((((((.......((.....(((((((....)))--)))).....))(((((((((((((........))).)))---.)))))---)).)).))))))))... ( -52.40)
>DroSim_CAF1 5390 100 + 1
CAG------------UUCCGGCGUCUGCAGCCUCAAGGGUCACCAUGGUG--ACCCCGACGGCGGUUGCCUGGGCAUCAACUGUUGCACCA---CGGCGG---CCAGCUCGGAGCUGUCC
(((------------(((((((.......(((((..(((((((....)))--)))).)).)))(((((((((((((........))).)))---.)))))---)).)).))))))))... ( -56.60)
>DroWil_CAF1 14708 118 + 1
CAGUGGAAGUGGAAGUUGCGGCAAUGUCAACACGAAAGGACAACUUCAUGAGAGCACGAA--AGGAUGCCUGGGCUUUGAUUGUUGCACCGCCAAGGCGGGAUCCAGUUCCGAAAUAUCC
...(((((.((((...((((((((((((....(....)))).........(((((.....--(((...)))..))))).)))))))))((((....))))..)))).)))))........ ( -38.90)
>DroYak_CAF1 5407 100 + 1
CAG------------UUCCGGCGUCGGUAGUCUCAAGGAUCACCAUGGUG--ACCACGACGGCGGCUGCCUGGGCAUCAACUGUUGCACCA---CGGCGG---CCAGCUCGGAGCUGUCC
(((------------(((((((((((...((((((.((....)).))).)--))..))))...(((((((((((((........))).)))---.)))))---)).)).))))))))... ( -51.30)
>consensus
CAG____________UUCCGGCGUCGGCAGCCUCAAGGGUCACCAUGGUG__ACCACGACGGCGGUUGCCUGGGCAUCAACUGUUGCACCA___CGGCGG___CCAGCUCGGAGCUGUCC
...............(((((((..............((..(((....)))...))........(((((((((((((........))).)))....)))))...)).)).)))))...... (-18.69 = -19.75 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	1,741,840 – 1,741,954
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	77.07
Mean single sequence MFE	-43.47
Consensus MFE	-24.10
Energy contribution	-27.10
Covariance contribution	3.00
Combinations/Pair	1.19
Mean z-score	-1.98
Structure conservation index	0.55
SVM decision value	0.29
SVM RNA-class probability	0.671108
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1741840 114 + 22407834
CUGUUGCACCA---CGGCGG---CCAGCUCGGAGCUGUCCAUCGACGAGACGUCAUCGACCUCGUCCAGAGGCUCCUGCGAGUUGACCAGCAAGGUGACCAACGACCUGAACGGAUUCCA
.(((((((((.---..((((---.(((((((.((..(((..(.((((((.((....))..)))))).)..)))..)).))))))).)).))..))))..))))).((.....))...... ( -40.90)
>DroSim_CAF1 5456 114 + 1
CUGUUGCACCA---CGGCGG---CCAGCUCGGAGCUGUCCAUCGACGAGACGUCAUCGACCUCGUCCAGGGGCUCCUCCGAGCUGACCAGCAAGGUGACCAAUGACCUGAACGGAUUCCA
(((((.((((.---..((((---.((((((((((..((((...((((((.((....))..))))))...))))..)))))))))).)).))..))))..((......)))))))...... ( -50.90)
>DroWil_CAF1 14786 111 + 1
UUGUUGCACCGCCAAGGCGGGAUCCAGUUCCGAAAUAUCCAUCGAUGAGACUGCAUCGACAUCUUCGCG---------CACUCUGGCAGCGAAAGUGAACAAUAAUCUGAGUAAUUUCGA
........((((....))))..........((((((.....((((((......))))))((..((((((---------(......)).)))))..))................)))))). ( -30.40)
>DroYak_CAF1 5473 114 + 1
CUGUUGCACCA---CGGCGG---CCAGCUCGGAGCUGUCCAUCGACGAGACGUCGUCGACCUCGUCCCGGGGCUCCUCCGAGCUGACCACCAAGGUGACCAAUGACCUGAGCGAAUUCCA
...((((....---.((.((---.((((((((((..((((...((((((.((....))..))))))...))))..)))))))))).)).)).((((........))))..))))...... ( -51.70)
>consensus
CUGUUGCACCA___CGGCGG___CCAGCUCGGAGCUGUCCAUCGACGAGACGUCAUCGACCUCGUCCAGGGGCUCCUCCGAGCUGACCACCAAGGUGACCAAUGACCUGAACGAAUUCCA
(((((.(.((.....)).).....((((((((((..((((...((((((...........))))))...))))..)))))))))).......((((........)))).)))))...... (-24.10 = -27.10 +   3.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:44 2006