Locus 1126

Sequence ID	3L_DroMel_CAF1
Location	3,291,478 – 3,291,590
Length	112
Max. P	0.880066

overview

Window 1

Location	3,291,478 – 3,291,590
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.41
Mean single sequence MFE	-43.68
Consensus MFE	-33.00
Energy contribution	-32.64
Covariance contribution	-0.36
Combinations/Pair	1.15
Mean z-score	-2.13
Structure conservation index	0.76
SVM decision value	0.91
SVM RNA-class probability	0.880066
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3291478 112 + 23771897
ACGUUGGCCGGGCCAACAGUGCCUAUCUGCGAUUUGGUACC--------UGUAUUCAACAAAUGCCGCUGGAAACGGGUAAAGGCCAGGUAGGGCCAUUUGGCACAGGCAUUUGGGCAGU
..((((((...)))))).(((((.(((...)))..)))))(--------(((......((((((((.(((....))).....((((......))))..........)))))))).)))). ( -42.20)
>DroSec_CAF1 21237 112 + 1
UCGUUGGCCGGGCCAACAGUGCCUAUCUGCGAUUUGGUACC--------UGUAUUCAACAAAUGCCGCUGGAAAUGGGUAAAGGCCAGGUAGGGCCAUUUGGCCCAGACAUUUGGACAGU
..(((.(((.((((.....(((((((.(.((...(((((..--------(((.....)))..))))).)).).)))))))..)))).))).(((((....))))).........)))... ( -38.20)
>DroSim_CAF1 22042 112 + 1
UCGUUGGCCGGGCCAACAGUGCCUAUCUGCGAUUUGGUACC--------UGUAUUCAACAAAUGCCGCUGGAAACGGGUAAAGGCCAGGUAGGGCCAUUUGGCCCAGACAUUUGGACAGU
..(((.(((.((((.((((((((.(((...)))..)))).)--------)))..........((((.(.(....))))))..)))).))).(((((....))))).........)))... ( -39.40)
>DroEre_CAF1 23296 112 + 1
UCGUUGGCCGGGCCAACAGUGCCUAUCUGCCAUUUGGUACC--------UGUAUUCAACAAAUGCCGGUGGAAACGGGUAAGGGCCAGGUAGGGCCGUUUGGCCCAGGCAUUCCAGCAGU
..(((((((((((((((.((.((((((((((......((((--------(((.((((.(.......).)))).)))))))..)).)))))))))).).))))))).)))....))))... ( -47.50)
>DroYak_CAF1 23961 120 + 1
UUGUUGGCCGGGCCAAAAACGCCUAUCUGCCAUUUGGUGCCAGUACCUGUGUGUUCAACAAAAGCCCGUGGAAACGGGUAAAGGCCAGGUAGGGCCAUUUGGCCCAGGCAUUUGAACAGU
(((((.(((((((((((....((((((((((....((((....))))..(((.....)))...((((((....))))))...)).))))))))....)))))))).))).....))))). ( -51.10)
>consensus
UCGUUGGCCGGGCCAACAGUGCCUAUCUGCGAUUUGGUACC________UGUAUUCAACAAAUGCCGCUGGAAACGGGUAAAGGCCAGGUAGGGCCAUUUGGCCCAGGCAUUUGGACAGU
..(((.(((.((((....(((((............)))))......................((((..((....))))))..)))).))).(((((....))))).........)))... (-33.00 = -32.64 +  -0.36)

alignment

secondary structure

dotplot

Window 2

Location	3,291,478 – 3,291,590
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.41
Mean single sequence MFE	-36.82
Consensus MFE	-29.42
Energy contribution	-29.82
Covariance contribution	0.40
Combinations/Pair	1.14
Mean z-score	-1.47
Structure conservation index	0.80
SVM decision value	0.15
SVM RNA-class probability	0.608175
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3291478 112 - 23771897
ACUGCCCAAAUGCCUGUGCCAAAUGGCCCUACCUGGCCUUUACCCGUUUCCAGCGGCAUUUGUUGAAUACA--------GGUACCAAAUCGCAGAUAGGCACUGUUGGCCCGGCCAACGU
.((((.....((((((((.(((((((((......)))).....((((.....)))).))))).....))))--------)))).......)))).........((((((...)))))).. ( -33.60)
>DroSec_CAF1 21237 112 - 1
ACUGUCCAAAUGUCUGGGCCAAAUGGCCCUACCUGGCCUUUACCCAUUUCCAGCGGCAUUUGUUGAAUACA--------GGUACCAAAUCGCAGAUAGGCACUGUUGGCCCGGCCAACGA
.(((((((((((((.(((((....)))))...((((.............)))).)))))))).........--------(((.....)))...)))))....(((((((...))))))). ( -34.32)
>DroSim_CAF1 22042 112 - 1
ACUGUCCAAAUGUCUGGGCCAAAUGGCCCUACCUGGCCUUUACCCGUUUCCAGCGGCAUUUGUUGAAUACA--------GGUACCAAAUCGCAGAUAGGCACUGUUGGCCCGGCCAACGA
.(((((.........(((((....)))))((((((........((((.....))))((.....))....))--------))))..........)))))....(((((((...))))))). ( -34.90)
>DroEre_CAF1 23296 112 - 1
ACUGCUGGAAUGCCUGGGCCAAACGGCCCUACCUGGCCCUUACCCGUUUCCACCGGCAUUUGUUGAAUACA--------GGUACCAAAUGGCAGAUAGGCACUGUUGGCCCGGCCAACGA
..((((....((((.(((((....)))))((((((........(((.......)))((.....))....))--------))))......))))....)))).(((((((...))))))). ( -38.70)
>DroYak_CAF1 23961 120 - 1
ACUGUUCAAAUGCCUGGGCCAAAUGGCCCUACCUGGCCUUUACCCGUUUCCACGGGCUUUUGUUGAACACACAGGUACUGGCACCAAAUGGCAGAUAGGCGUUUUUGGCCCGGCCAACAA
..((((.....(((.((((((((..(((.((((((.......(((((....)))))....(((.....)))))))))(((.((.....)).)))...)))...))))))))))).)))). ( -42.60)
>consensus
ACUGUCCAAAUGCCUGGGCCAAAUGGCCCUACCUGGCCUUUACCCGUUUCCAGCGGCAUUUGUUGAAUACA________GGUACCAAAUCGCAGAUAGGCACUGUUGGCCCGGCCAACGA
.((((.((((((((.(((((....)))))...((((.............)))).)))))))).................(....).....))))........(((((((...))))))). (-29.42 = -29.82 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:48 2006