Locus 1730

Sequence ID	2R_DroMel_CAF1
Location	6,511,791 – 6,511,888
Length	97
Max. P	0.818846

overview

Window 3

Location	6,511,791 – 6,511,888
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.01
Mean single sequence MFE	-35.32
Consensus MFE	-20.40
Energy contribution	-21.52
Covariance contribution	1.11
Combinations/Pair	1.15
Mean z-score	-2.02
Structure conservation index	0.58
SVM decision value	0.67
SVM RNA-class probability	0.818846
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6511791 97 + 20766785
UAUCAGCCAGUCACUAGUCACUCGAUUUGGCAAUAACAAUAAGCCA-GACAAGGAGCUGUGGGCCACCAGC---GGGUGG---CCU-GAUGGCUGAUGGCU-CUGG--------------
(((((((((..(((.(((..((.(.((((((...........))))-))).))..))))))(((((((...---.)))))---)).-..)))))))))...-....-------------- ( -42.30)
>DroPse_CAF1 76210 89 + 1
CAUCAAC-AUCAACUAGUCACUCGGUUUGGCAAUAACAAUAAGCCAAGACAAGCU------GGCC---AGAGCAGGGUGGCGGUGUGGAGGGGUGGCGG---------------------
((((...-.((.(((.((((((((.((((((..........(((........)))------.)))---))).).))))))))))...))..))))....--------------------- ( -26.90)
>DroSec_CAF1 78931 100 + 1
UAUCAGCCAGUCACUAGUCACUCGAUUUGGCAAUAACAAUAAGCCA-GACAAGGAGCUGUGGGCC---AGC---GGGUGG---GCU-GAUGGCUGAUGGCU-CUGG--------CUCUCC
....((((.(((...((((....))))((((...........))))-)))..((((((((.((((---(.(---((....---.))-).))))).))))))-))))--------)).... ( -37.10)
>DroSim_CAF1 65311 108 + 1
UAUCAGCCAGUCACUAGUCACUCGAUUUGGCAAUAACAAUAAGCCA-GACAAGGAGCUGUGGGCC---AGC---GGGUGG---GCU-GAUGGCUGAUGGCU-CUGGCUCUAUGGCUCUCC
....(((((......((((....(.((((((...........))))-)))..((((((((.((((---(.(---((....---.))-).))))).))))))-))))))...))))).... ( -39.00)
>DroEre_CAF1 80576 87 + 1
UAUCAGCCAGUCACUAGUCACUCGAUUUGGCAAUAACAAUAAGCCA-GACAAGGAGCUGUGGGCC---AGC---GGGCGG---UCC-GAUGGCUGAUG----------------------
(((((((((.((..((((..((.(.((((((...........))))-))).))..)))).(((((---...---....))---)))-)))))))))))---------------------- ( -33.10)
>DroYak_CAF1 83139 95 + 1
UAUCAGCCAGUCACUAGUCACUCGAUUUGGCAAUAACAAUAAGCCA-GACAAGGAGCUGUGGGCC---AGC---GGGUGG---GCU-GAUGGCUGAUGGCUUCUGG--------------
(((((((((.((((.(((..((.(.((((((...........))))-))).))..)))))))..(---(((---......---)))-).)))))))))........-------------- ( -33.50)
>consensus
UAUCAGCCAGUCACUAGUCACUCGAUUUGGCAAUAACAAUAAGCCA_GACAAGGAGCUGUGGGCC___AGC___GGGUGG___GCU_GAUGGCUGAUGGCU_CUGG______________
(((((((((.((((.(((..((.(...((((...........))))...).))..)))))))(((..........)))...........)))))))))...................... (-20.40 = -21.52 +   1.11)

alignment

secondary structure

dotplot

Window 4

Location	6,511,791 – 6,511,888
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.01
Mean single sequence MFE	-30.25
Consensus MFE	-18.66
Energy contribution	-20.52
Covariance contribution	1.86
Combinations/Pair	1.04
Mean z-score	-1.54
Structure conservation index	0.62
SVM decision value	0.21
SVM RNA-class probability	0.633150
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6511791 97 - 20766785
--------------CCAG-AGCCAUCAGCCAUC-AGG---CCACCC---GCUGGUGGCCCACAGCUCCUUGUC-UGGCUUAUUGUUAUUGCCAAAUCGAGUGACUAGUGACUGGCUGAUA
--------------....-....((((((((..-.((---(((((.---...)))))))(((((.((((((..-((((...........))))...)))).)))).)))..)))))))). ( -39.50)
>DroPse_CAF1 76210 89 - 1
---------------------CCGCCACCCCUCCACACCGCCACCCUGCUCU---GGCC------AGCUUGUCUUGGCUUAUUGUUAUUGCCAAACCGAGUGACUAGUUGAU-GUUGAUG
---------------------..........((.(((.(((((........)---))).------.(((((..(((((...........)))))..)))))........).)-)).)).. ( -18.50)
>DroSec_CAF1 78931 100 - 1
GGAGAG--------CCAG-AGCCAUCAGCCAUC-AGC---CCACCC---GCU---GGCCCACAGCUCCUUGUC-UGGCUUAUUGUUAUUGCCAAAUCGAGUGACUAGUGACUGGCUGAUA
((....--------))..-....((((((((((-(((---......---)))---))..(((((.((((((..-((((...........))))...)))).)))).)))..)))))))). ( -31.30)
>DroSim_CAF1 65311 108 - 1
GGAGAGCCAUAGAGCCAG-AGCCAUCAGCCAUC-AGC---CCACCC---GCU---GGCCCACAGCUCCUUGUC-UGGCUUAUUGUUAUUGCCAAAUCGAGUGACUAGUGACUGGCUGAUA
((...((......))...-..))((((((((((-(((---......---)))---))..(((((.((((((..-((((...........))))...)))).)))).)))..)))))))). ( -32.40)
>DroEre_CAF1 80576 87 - 1
----------------------CAUCAGCCAUC-GGA---CCGCCC---GCU---GGCCCACAGCUCCUUGUC-UGGCUUAUUGUUAUUGCCAAAUCGAGUGACUAGUGACUGGCUGAUA
----------------------.((((((((((-((.---....))---(((---(.....))))((((((..-((((...........))))...)))).)).....)).)))))))). ( -29.20)
>DroYak_CAF1 83139 95 - 1
--------------CCAGAAGCCAUCAGCCAUC-AGC---CCACCC---GCU---GGCCCACAGCUCCUUGUC-UGGCUUAUUGUUAUUGCCAAAUCGAGUGACUAGUGACUGGCUGAUA
--------------.........((((((((((-(((---......---)))---))..(((((.((((((..-((((...........))))...)))).)))).)))..)))))))). ( -30.60)
>consensus
______________CCAG_AGCCAUCAGCCAUC_AGC___CCACCC___GCU___GGCCCACAGCUCCUUGUC_UGGCUUAUUGUUAUUGCCAAAUCGAGUGACUAGUGACUGGCUGAUA
.......................((((((((..................((.....)).(((((.((((((...((((...........))))...)))).)))).)))..)))))))). (-18.66 = -20.52 +   1.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:56 2006