Locus 5597

Sequence ID	2R_DroMel_CAF1
Location	17,865,683 – 17,865,793
Length	110
Max. P	0.999586

overview

Window 3

Location	17,865,683 – 17,865,793
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.91
Mean single sequence MFE	-16.42
Consensus MFE	-14.17
Energy contribution	-14.13
Covariance contribution	-0.04
Combinations/Pair	1.06
Mean z-score	-2.28
Structure conservation index	0.86
SVM decision value	2.25
SVM RNA-class probability	0.991108
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17865683 110 + 20766785
UUUAUUUCGUUUUAUUCCUUCGUUUUUAUUACGGUCCUGCCCCAAGGCAACGACACAUUUCUGCCAAAUGUUUCUCCAUUUAUCCUUUUGGCCCUCCCAUCACGAUUCCC
......((((..........(((.......)))(((.((((....))))..)))........((((((..................)))))).........))))..... ( -15.97)
>DroSec_CAF1 31000 110 + 1
UUUAUUUCGUUUUAUUCCUCCGUUUUUAUUACGGUCCUGCCCCAAGGCAACGACACAUUUCUGCCAAAUGUUUCUCCAUUUAUCCUUUUGGCCCUCCCAUCAGGAUUCUC
......(((((........((((.......))))....(((....)))))))).((((((.....))))))..........(((((..(((.....)))..))))).... ( -19.80)
>DroSim_CAF1 31333 110 + 1
UUUAUUUCGUUUUAUUCCUUCGUUUUUAUUACGGUCCUGCCCCAAGGCAACGACACAUUUCUGCCAAAUGUUUCUCAAUUUAUCCUUUUGGCCCUCCCAUCACGAUUCCC
......((((..........(((.......)))(((.((((....))))..)))........((((((..................)))))).........))))..... ( -15.97)
>DroEre_CAF1 33480 110 + 1
UUUAUUUCGUUUUAUUCCUCCGUUUUUAUUACGGUCCUGCCCCAAGGCAACGACACAUUUCUGCCAAAUGUUUCUCCAUUUAUCCUUUUGGCCCUCCCAUCCCGAUUACC
......(((((........((((.......))))....(((....)))))))).........((((((..................)))))).................. ( -16.07)
>DroYak_CAF1 29677 110 + 1
UUUAUUCCGUUUUAUUCCUUCGUUUUUAUUACGGUCCUGCCCCAAGGCAACGACACAUUUCUGCCAAAUGUUUCUCCAUUUAUCCUUUUGGCCCUCCCAUCCCGAUUACC
...................(((...........(((.((((....))))..)))........((((((..................))))))..........)))..... ( -14.27)
>consensus
UUUAUUUCGUUUUAUUCCUUCGUUUUUAUUACGGUCCUGCCCCAAGGCAACGACACAUUUCUGCCAAAUGUUUCUCCAUUUAUCCUUUUGGCCCUCCCAUCACGAUUCCC
......(((((........((((.......))))....(((....)))))))).........((((((..................)))))).................. (-14.17 = -14.13 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	17,865,683 – 17,865,793
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.91
Mean single sequence MFE	-25.74
Consensus MFE	-22.88
Energy contribution	-23.12
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-3.12
Structure conservation index	0.89
SVM decision value	3.75
SVM RNA-class probability	0.999586
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17865683 110 - 20766785
GGGAAUCGUGAUGGGAGGGCCAAAAGGAUAAAUGGAGAAACAUUUGGCAGAAAUGUGUCGUUGCCUUGGGGCAGGACCGUAAUAAAAACGAAGGAAUAAAACGAAAUAAA
.....((((.((((....(((..((((...(((((....((((((.....)))))).))))).))))..)))....))))........(....)......))))...... ( -27.00)
>DroSec_CAF1 31000 110 - 1
GAGAAUCCUGAUGGGAGGGCCAAAAGGAUAAAUGGAGAAACAUUUGGCAGAAAUGUGUCGUUGCCUUGGGGCAGGACCGUAAUAAAAACGGAGGAAUAAAACGAAAUAAA
.....((((.........(((..((((...(((((....((((((.....)))))).))))).))))..)))....((((.......))))))))............... ( -27.00)
>DroSim_CAF1 31333 110 - 1
GGGAAUCGUGAUGGGAGGGCCAAAAGGAUAAAUUGAGAAACAUUUGGCAGAAAUGUGUCGUUGCCUUGGGGCAGGACCGUAAUAAAAACGAAGGAAUAAAACGAAAUAAA
.....((((.((((....(((..((((.(((.....((.((((((.....)))))).)).)))))))..)))....))))........(....)......))))...... ( -24.30)
>DroEre_CAF1 33480 110 - 1
GGUAAUCGGGAUGGGAGGGCCAAAAGGAUAAAUGGAGAAACAUUUGGCAGAAAUGUGUCGUUGCCUUGGGGCAGGACCGUAAUAAAAACGGAGGAAUAAAACGAAAUAAA
.....(((..........(((..((((...(((((....((((((.....)))))).))))).))))..)))....((((.......))))..........)))...... ( -25.20)
>DroYak_CAF1 29677 110 - 1
GGUAAUCGGGAUGGGAGGGCCAAAAGGAUAAAUGGAGAAACAUUUGGCAGAAAUGUGUCGUUGCCUUGGGGCAGGACCGUAAUAAAAACGAAGGAAUAAAACGGAAUAAA
.....(((..((((....(((..((((...(((((....((((((.....)))))).))))).))))..)))....))))........(....).......)))...... ( -25.20)
>consensus
GGGAAUCGUGAUGGGAGGGCCAAAAGGAUAAAUGGAGAAACAUUUGGCAGAAAUGUGUCGUUGCCUUGGGGCAGGACCGUAAUAAAAACGAAGGAAUAAAACGAAAUAAA
.....(((..((((....(((..((((...(((((....((((((.....)))))).))))).))))..)))....))))........(....).......)))...... (-22.88 = -23.12 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:31 2006