Locus 4857

Sequence ID	2L_DroMel_CAF1
Location	13,812,362 – 13,812,458
Length	96
Max. P	0.943806

overview

Window 4

Location	13,812,362 – 13,812,458
Length	96
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	81.39
Mean single sequence MFE	-19.24
Consensus MFE	-12.09
Energy contribution	-12.29
Covariance contribution	0.20
Combinations/Pair	1.19
Mean z-score	-2.44
Structure conservation index	0.63
SVM decision value	1.34
SVM RNA-class probability	0.943806
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13812362 96 + 22407834
UUUGUCAGCUAAAGUUGGUUUGUAAAUGGUGCAGGAAAUCCAAU--------CUAUCAUUGCAUCAUCUACGAACAAACCUACAACUCUUUCAAACUAACCAUU
.((((((((....))))(((((((.(((((((((((........--------...)).))))))))).)))))))......))))................... ( -21.30)
>DroSec_CAF1 312 95 + 1
UUUGUCAGCUAAA-UUAGCUUGUAAAUGGUGCAGGAAAUCCAAU--------CUAUCAUUGUACCAUCUACGAACAAAUCUACAAAUCUUUCAAACUAACCAUU
(((((..((((..-.))))(((((.(((((((((((........--------...)).))))))))).)))))))))).......................... ( -17.70)
>DroSim_CAF1 312 95 + 1
UUUGUCAGCUAAA-UUAGCUUGUAAAUGGUGCAGGAAAUCCAAU--------CUAUCAUUGUACCAUCUACGAACAAAUCUACAAAUCUUUCAAACUAACCAUU
(((((..((((..-.))))(((((.(((((((((((........--------...)).))))))))).)))))))))).......................... ( -17.70)
>DroEre_CAF1 312 103 + 1
UUUGUUACCUAAA-GCUGCUUGUAAAUGGUGCAGGAAAUCCGAUUCAAAACACUAUCACUGCCCCAUUUACGAAGAGACCUACAGCACUGUGAAACUAACCAUU
.............-((((.((((((((((.(((((....))(((..........)))..))).))))))))))((....)).)))).................. ( -21.50)
>DroYak_CAF1 312 102 + 1
UUUGUCACUUAAA-GCUGCUUAUAAAUGGUGCAGGAAAUCCGAUUCAAAACAUUAUCACUGCC-CAUUUACGAAGAUAUCUACAGCUCCUUGAAACUAAACAUU
....(((.....(-((((.(..(((((((.(((((....))(((..........)))..))))-))))))..)((....)).)))))...)))........... ( -18.00)
>consensus
UUUGUCAGCUAAA_UUAGCUUGUAAAUGGUGCAGGAAAUCCAAU________CUAUCAUUGCACCAUCUACGAACAAAUCUACAACUCUUUCAAACUAACCAUU
...................(((((.(((((((((((...................)).))))))))).)))))............................... (-12.09 = -12.29 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	13,812,362 – 13,812,458
Length	96
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	81.39
Mean single sequence MFE	-23.88
Consensus MFE	-15.56
Energy contribution	-16.40
Covariance contribution	0.84
Combinations/Pair	1.30
Mean z-score	-1.65
Structure conservation index	0.65
SVM decision value	0.02
SVM RNA-class probability	0.542028
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13812362 96 - 22407834
AAUGGUUAGUUUGAAAGAGUUGUAGGUUUGUUCGUAGAUGAUGCAAUGAUAG--------AUUGGAUUUCCUGCACCAUUUACAAACCAACUUUAGCUGACAAA
....(((((((....((((((...(((((((..((((..(((.((((.....--------)))).)))..)))).......))))))))))))))))))))... ( -24.10)
>DroSec_CAF1 312 95 - 1
AAUGGUUAGUUUGAAAGAUUUGUAGAUUUGUUCGUAGAUGGUACAAUGAUAG--------AUUGGAUUUCCUGCACCAUUUACAAGCUAA-UUUAGCUGACAAA
....((((((((....))....((((((.(((.(((((((((.((.......--------...((....)))).))))))))).))).))-))))))))))... ( -21.00)
>DroSim_CAF1 312 95 - 1
AAUGGUUAGUUUGAAAGAUUUGUAGAUUUGUUCGUAGAUGGUACAAUGAUAG--------AUUGGAUUUCCUGCACCAUUUACAAGCUAA-UUUAGCUGACAAA
....((((((((....))....((((((.(((.(((((((((.((.......--------...((....)))).))))))))).))).))-))))))))))... ( -21.00)
>DroEre_CAF1 312 103 - 1
AAUGGUUAGUUUCACAGUGCUGUAGGUCUCUUCGUAAAUGGGGCAGUGAUAGUGUUUUGAAUCGGAUUUCCUGCACCAUUUACAAGCAGC-UUUAGGUAACAAA
....((((.((.......(((((.((.....))((((((((.((((.((....((((......)))).)))))).))))))))..)))))-...)).))))... ( -25.70)
>DroYak_CAF1 312 102 - 1
AAUGUUUAGUUUCAAGGAGCUGUAGAUAUCUUCGUAAAUG-GGCAGUGAUAAUGUUUUGAAUCGGAUUUCCUGCACCAUUUAUAAGCAGC-UUUAAGUGACAAA
........(((....((((((((.((.....))(((((((-(((((.((...((........))....)))))).))))))))..)))))-)))....)))... ( -27.60)
>consensus
AAUGGUUAGUUUGAAAGAGUUGUAGAUUUGUUCGUAGAUGGUGCAAUGAUAG________AUUGGAUUUCCUGCACCAUUUACAAGCAAA_UUUAGCUGACAAA
....(((((((......((((...((.....))((((((((((((..(((..........)))((....)))))))))))))).))))......)))))))... (-15.56 = -16.40 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:27 2006