Locus 4050

Sequence ID	2R_DroMel_CAF1
Location	13,368,180 – 13,368,295
Length	115
Max. P	0.685185

overview

Window 5

Location	13,368,180 – 13,368,295
Length	115
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	86.16
Mean single sequence MFE	-36.17
Consensus MFE	-23.11
Energy contribution	-24.30
Covariance contribution	1.19
Combinations/Pair	1.24
Mean z-score	-2.09
Structure conservation index	0.64
SVM decision value	0.32
SVM RNA-class probability	0.685185
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13368180 115 + 20766785
AUGUACCAUCCGCCUUAUUUGGGAUGCAGUUCCUCCUCCUGCUUCUUCUGACC---UCAUCUGCGUAUUCAAAUGAAGGGAAGAAGGGGCUUCAGAGGAACCUCUACGUAACGGACAA
(((((.(((((..........)))))..(((((((.....(((((((((..((---((((.((......)).))).)))..)))))))))....)))))))...)))))......... ( -37.40)
>DroSec_CAF1 66995 118 + 1
AUGUAUCUCCCACCUUAUUUGGCAUGCAGUUCCUCCUCCUGUUUCUUCUGACCUUCUCAUCCGCGUAUUCACAUGAAGGGAAGAAGGGGCUUCAGAGGAACCUCUACGUAACGGACAA
.(((((...(((.......))).)))))(((((((.....((..(((((..(((((..................)))))..)))))..))....)))))))................. ( -33.67)
>DroEre_CAF1 67942 118 + 1
AUGUGCUUCCCGCCUCAUUGGCGAUGCAGUUCCUCCUACUGCUUCUUCUGACCUUCUCAUCUGCUUAUUCGAAUGAAGGGAAGAAAGGGCUUCAGAGGACCCUCUACAUAACGGACAA
.(((.(....((((.....))))(((.((.(((((.....(((..((((..(((((...((.........))..)))))..))))..)))....)))))....)).)))...).))). ( -35.00)
>DroYak_CAF1 69174 118 + 1
AUGUGCUUCCCGCCUCAUCGGGGAUGCAGUUCCUCCUACUGUUGCUGCUGAGCUUCUCAUCUGCUUAUUCAAAUAAAGGGCAGGAGGAGCUUCAGAGGAACCUCUACAUAACGGACAA
((((((((((((......)))))).)).(((((((.....((....)).(((((((((..((((((...........)))))))))))))))..)))))))....))))......... ( -38.60)
>consensus
AUGUACCUCCCGCCUCAUUGGGGAUGCAGUUCCUCCUACUGCUUCUUCUGACCUUCUCAUCUGCGUAUUCAAAUGAAGGGAAGAAGGGGCUUCAGAGGAACCUCUACAUAACGGACAA
(((((...((((......))))......(((((((.....(((((((((..(((..((((.((......)).)))))))..)))))))))....)))))))...)))))......... (-23.11 = -24.30 +   1.19)

alignment

secondary structure

dotplot

Window 6

Location	13,368,180 – 13,368,295
Length	115
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	86.16
Mean single sequence MFE	-37.41
Consensus MFE	-24.85
Energy contribution	-26.23
Covariance contribution	1.37
Combinations/Pair	1.17
Mean z-score	-1.57
Structure conservation index	0.66
SVM decision value	0.00
SVM RNA-class probability	0.533609
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13368180 115 - 20766785
UUGUCCGUUACGUAGAGGUUCCUCUGAAGCCCCUUCUUCCCUUCAUUUGAAUACGCAGAUGA---GGUCAGAAGAAGCAGGAGGAGGAACUGCAUCCCAAAUAAGGCGGAUGGUACAU
.((((((((.(((...(((((((((....((.(((((((.(((((((((......)))))))---))...)))))))..)).)))))))))..............)))))))).))). ( -41.03)
>DroSec_CAF1 66995 118 - 1
UUGUCCGUUACGUAGAGGUUCCUCUGAAGCCCCUUCUUCCCUUCAUGUGAAUACGCGGAUGAGAAGGUCAGAAGAAACAGGAGGAGGAACUGCAUGCCAAAUAAGGUGGGAGAUACAU
.(.(((........(.(((((((((....((.(((((..(((((.((((....)))).....)))))..))))).....)).))))))))).)..(((......))).))).)..... ( -34.10)
>DroEre_CAF1 67942 118 - 1
UUGUCCGUUAUGUAGAGGGUCCUCUGAAGCCCUUUCUUCCCUUCAUUCGAAUAAGCAGAUGAGAAGGUCAGAAGAAGCAGUAGGAGGAACUGCAUCGCCAAUGAGGCGGGAAGCACAU
...(((...((((((....((((((...((..(((((..(((((..((.........))...)))))..)))))..))....)))))).))))))((((.....)))))))....... ( -36.70)
>DroYak_CAF1 69174 118 - 1
UUGUCCGUUAUGUAGAGGUUCCUCUGAAGCUCCUCCUGCCCUUUAUUUGAAUAAGCAGAUGAGAAGCUCAGCAGCAACAGUAGGAGGAACUGCAUCCCCGAUGAGGCGGGAAGCACAU
......(((...(((((....))))).)))(((((((((..((((((((......))))))))..(((....)))....)))))))))..(((.(((((......).)))).)))... ( -37.80)
>consensus
UUGUCCGUUACGUAGAGGUUCCUCUGAAGCCCCUUCUUCCCUUCAUUUGAAUAAGCAGAUGAGAAGGUCAGAAGAAACAGGAGGAGGAACUGCAUCCCAAAUAAGGCGGGAAGCACAU
...((((((((((...(((((((((.......(((((((((((((((((......)))))))..)))...))))))).....))))))))))))).........))))))........ (-24.85 = -26.23 +   1.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:32 2006