Locus 5008

Sequence ID	2L_DroMel_CAF1
Location	14,392,320 – 14,392,422
Length	102
Max. P	0.659956

overview

Window 0

Location	14,392,320 – 14,392,422
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.17
Mean single sequence MFE	-59.38
Consensus MFE	-29.59
Energy contribution	-29.90
Covariance contribution	0.31
Combinations/Pair	1.16
Mean z-score	-1.86
Structure conservation index	0.50
SVM decision value	0.27
SVM RNA-class probability	0.659956
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14392320 102 + 22407834
GGCGGCGGCGAGGGCGGCUUCCUGCAGGCGAUUCGAGCUGGCG---AUUUGGGCAGCCGCCGCCGCUGCCGCU------------GCCGCUGCACUGGGACUGUGCAUGG---CGGCCGA
(((((((((...(((((((.(((((.(((.......))).)).---....))).))))))))))))))))(((------------((((.(((((.......))))))))---))))... ( -62.60)
>DroPse_CAF1 22070 117 + 1
GGCGGCGGCCAUGGCCGCCUCCUGGAGGCGAUUGGAGCUGGCCUGAGCCUGGGCCGCCUGGGCGG---CUGCUGCAUGGGCAUGGGCUGCUGCACUGGGGCUGUGCAUGGUUGCUGCCGA
(((((((((((((((((((((...)))))...((.(((.((((((.(((((((((((....))))---))......))))).))))))))).))....)))....))))))))))))).. ( -66.90)
>DroEre_CAF1 13426 99 + 1
GGCGGCGGCGAUGGCGGCUUCCUGCAGGCGAUUCGAGCUGGCG---AUUUGGGCCGCCGCCGCAG---CCGCU------------GCCGCUGCACUGGGACUAUGCAUGG---CGGCCGA
(((((((((..(((((((..(((((.(((.......))).)).---....)))..)))))))..)---)))))------------)))(((((..((........))..)---))))... ( -52.20)
>DroYak_CAF1 13159 99 + 1
GGCGGCGGCGAGGGCGGCUUCCUGCAGGCGAUUGGAGCUGGCG---AUUUGGGCAGCCGCCGCAG---CCGCU------------GCCGCUGCACUGGGACUGUGCAUGG---CGGCCGA
(((((((((...(((((((.(((((.(((.......))).)).---....))).)))))))...)---)))))------------((((.(((((.......))))))))---).))).. ( -54.80)
>DroAna_CAF1 28601 99 + 1
GGCAGCGGCCAGAGCCGCCUCCUGGAGGCGAUUUGAGCUGGCU---GCGGCCACUGCAGCUGCAG---CAGCU------------GCCGCUGCACUGGGGCUGUGCAUCG---AGGCGGA
(((((((((((((..((((((...)))))).)))).))).(((---(((((.......)))))))---).)))------------))).((((.((.((((...)).)).---)))))). ( -52.30)
>DroPer_CAF1 24291 117 + 1
GGCGGCGGCCAUGGCCGCCUCCUGGAGGCGAUUGGAGCUGGCCUGCGCCUGGGCCGCCUGGGCGG---CUGCUGCAUGGGCAUGGGCUGCUGCACUGGGGCUGUGCAUGGUUGCUGCCGA
(((((((((((((((((((((...)))))...((.(((.(((((..(((((((((((....))))---))......)))))..)))))))).))....)))....))))))))))))).. ( -67.50)
>consensus
GGCGGCGGCCAGGGCCGCCUCCUGCAGGCGAUUGGAGCUGGCG___ACUUGGGCCGCCGCCGCAG___CCGCU____________GCCGCUGCACUGGGACUGUGCAUGG___CGGCCGA
(((((((((...(((.((((.....))))..........(((..........))))))...((.......)).............))))))((((.......)))).........))).. (-29.59 = -29.90 +   0.31)

alignment

secondary structure

dotplot

Window 1

Location	14,392,320 – 14,392,422
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.17
Mean single sequence MFE	-49.73
Consensus MFE	-24.08
Energy contribution	-25.30
Covariance contribution	1.22
Combinations/Pair	1.16
Mean z-score	-1.82
Structure conservation index	0.48
SVM decision value	0.05
SVM RNA-class probability	0.559508
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14392320 102 - 22407834
UCGGCCG---CCAUGCACAGUCCCAGUGCAGCGGC------------AGCGGCAGCGGCGGCGGCUGCCCAAAU---CGCCAGCUCGAAUCGCCUGCAGGAAGCCGCCCUCGCCGCCGCC
...((((---(..(((((.......))))))))))------------.(((((.((((.(((((((..((....---.((..((.......))..)).)).))))))).)))).))))). ( -52.50)
>DroPse_CAF1 22070 117 - 1
UCGGCAGCAACCAUGCACAGCCCCAGUGCAGCAGCCCAUGCCCAUGCAGCAG---CCGCCCAGGCGGCCCAGGCUCAGGCCAGCUCCAAUCGCCUCCAGGAGGCGGCCAUGGCCGCCGCC
..(((.(((....(((((.......)))))(((.....)))...)))(((.(---((((....)))))...(((....))).)))......)))....((.((((((....)))))).)) ( -52.00)
>DroEre_CAF1 13426 99 - 1
UCGGCCG---CCAUGCAUAGUCCCAGUGCAGCGGC------------AGCGG---CUGCGGCGGCGGCCCAAAU---CGCCAGCUCGAAUCGCCUGCAGGAAGCCGCCAUCGCCGCCGCC
...((((---(..(((((.......))))))))))------------.((((---(.(((..((((((((....---.((..((.......))..)).))..))))))..))).))))). ( -47.40)
>DroYak_CAF1 13159 99 - 1
UCGGCCG---CCAUGCACAGUCCCAGUGCAGCGGC------------AGCGG---CUGCGGCGGCUGCCCAAAU---CGCCAGCUCCAAUCGCCUGCAGGAAGCCGCCCUCGCCGCCGCC
...((((---(..(((((.......))))))))))------------.((((---(.(((((((((..((....---.((..((.......))..)).)).)))))))...)).))))). ( -46.50)
>DroAna_CAF1 28601 99 - 1
UCCGCCU---CGAUGCACAGCCCCAGUGCAGCGGC------------AGCUG---CUGCAGCUGCAGUGGCCGC---AGCCAGCUCAAAUCGCCUCCAGGAGGCGGCUCUGGCCGCUGCC
...(((.---...(((((.......)))))..)))------------(((((---...)))))((((((((((.---((((.(.......)(((((...))))))))).)))))))))). ( -48.20)
>DroPer_CAF1 24291 117 - 1
UCGGCAGCAACCAUGCACAGCCCCAGUGCAGCAGCCCAUGCCCAUGCAGCAG---CCGCCCAGGCGGCCCAGGCGCAGGCCAGCUCCAAUCGCCUCCAGGAGGCGGCCAUGGCCGCCGCC
..(((.(((....(((((.......)))))(((.....)))...)))(((.(---((((....)))))...(((....))).)))......)))....((.((((((....)))))).)) ( -51.80)
>consensus
UCGGCCG___CCAUGCACAGCCCCAGUGCAGCGGC____________AGCGG___CUGCGGCGGCGGCCCAAAC___CGCCAGCUCCAAUCGCCUCCAGGAAGCCGCCAUCGCCGCCGCC
..(((........(((((.......)))))(((((.............((.......))((((((.((..........))............((....))..))))))...))))).))) (-24.08 = -25.30 +   1.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:22 2006