Locus 1180

Sequence ID	3R_DroMel_CAF1
Location	3,569,202 – 3,569,311
Length	109
Max. P	0.718019

overview

Window 1

Location	3,569,202 – 3,569,311
Length	109
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	93.24
Mean single sequence MFE	-22.24
Consensus MFE	-18.50
Energy contribution	-18.58
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.31
Structure conservation index	0.83
SVM decision value	0.05
SVM RNA-class probability	0.559205
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3569202 109 + 27905053
AAAAAUCAAGCUCAACUCAUUUUACAGCCCCAUAAGGAGAAAGUCCGACCAGGUCAGAGCGUUGACCGCACCCUUUCCCUAGCGAAACCCACUU-UCCUCGAUUUUCCCU
.((((((..(((.............))).......(..((((((.......((((((....))))))((............)).......))))-))..))))))).... ( -17.92)
>DroSec_CAF1 20178 109 + 1
AAAAAUCAAGCUCAACUCAUGUUACAGCCCCAUAAGGAGAAAGUCCGAGCAGGUCAGAGCGUUGACCGCACCCUUUCCCUAGCGAAACCCACUU-UCCUCGAUUUUUCCU
(((((((..(((.(((....)))..))).......(..((((((....((.((((((....))))))))....((((......))))...))))-))..))))))))... ( -22.60)
>DroSim_CAF1 20487 109 + 1
AAAAAUCAAGCUCAACUCAUGUUACAGCCCCAUAAGGAGAAAGUCCGAGCAGGUCAGAGCGUUGACCGCACCCUUUCCCUAGCGAAACCCACUU-UCCUCGAUUUUUCCU
(((((((..(((.(((....)))..))).......(..((((((....((.((((((....))))))))....((((......))))...))))-))..))))))))... ( -22.60)
>DroEre_CAF1 25578 109 + 1
AAAAAUCAAGCUGAACUCAAGUAACAGCCCCUUAAGGAGAAAGUCCGAGCAGGUCAGAGCGUUGACCGCACCCUUUCCCUACCGAACCCCACUU-UUCUCGAUUUUUCCU
(((((((..((((.((....))..))))......(((.(((((...(.((.((((((....)))))))).).))))))))..............-.....)))))))... ( -23.70)
>DroYak_CAF1 12920 110 + 1
AAAAAUCAAGCUGAACUCAUUUAACAGCCCCAUAAGGAGAAAGUCCGUGUAGGUCAGAUCGUUGACCGCAUCCUUUCCCUACCAAAACCCACUUUUUCUCGAUUUUUCCU
(((((((..((((...........))))......(((.(((((...((((.((((((....)))))))))).))))))))....................)))))))... ( -24.40)
>consensus
AAAAAUCAAGCUCAACUCAUGUUACAGCCCCAUAAGGAGAAAGUCCGAGCAGGUCAGAGCGUUGACCGCACCCUUUCCCUAGCGAAACCCACUU_UCCUCGAUUUUUCCU
(((((((..(((.............)))......(((.(((((...(.((.((((((....)))))))).).))))))))....................)))))))... (-18.50 = -18.58 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	3,569,202 – 3,569,311
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	93.24
Mean single sequence MFE	-33.70
Consensus MFE	-28.18
Energy contribution	-28.78
Covariance contribution	0.60
Combinations/Pair	1.11
Mean z-score	-1.42
Structure conservation index	0.84
SVM decision value	0.39
SVM RNA-class probability	0.718019
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3569202 109 - 27905053
AGGGAAAAUCGAGGA-AAGUGGGUUUCGCUAGGGAAAGGGUGCGGUCAACGCUCUGACCUGGUCGGACUUUCUCCUUAUGGGGCUGUAAAAUGAGUUGAGCUUGAUUUUU
...((((((((((((-....(((((..((((((...((((((.......))))))..))))))..)))))..)))))...(((((.(((......))))))))))))))) ( -33.50)
>DroSec_CAF1 20178 109 - 1
AGGAAAAAUCGAGGA-AAGUGGGUUUCGCUAGGGAAAGGGUGCGGUCAACGCUCUGACCUGCUCGGACUUUCUCCUUAUGGGGCUGUAACAUGAGUUGAGCUUGAUUUUU
...((((((((((..-.....(((..((..((((((((.(.(((((((......))))).)).)...))))).)))..))..))).((((....))))..)))))))))) ( -34.60)
>DroSim_CAF1 20487 109 - 1
AGGAAAAAUCGAGGA-AAGUGGGUUUCGCUAGGGAAAGGGUGCGGUCAACGCUCUGACCUGCUCGGACUUUCUCCUUAUGGGGCUGUAACAUGAGUUGAGCUUGAUUUUU
...((((((((((..-.....(((..((..((((((((.(.(((((((......))))).)).)...))))).)))..))..))).((((....))))..)))))))))) ( -34.60)
>DroEre_CAF1 25578 109 - 1
AGGAAAAAUCGAGAA-AAGUGGGGUUCGGUAGGGAAAGGGUGCGGUCAACGCUCUGACCUGCUCGGACUUUCUCCUUAAGGGGCUGUUACUUGAGUUCAGCUUGAUUUUU
...((((((((((((-......(((((((((((...((((((.......))))))..))))).)))))))))))......((((((..((....)).))))))))))))) ( -36.60)
>DroYak_CAF1 12920 110 - 1
AGGAAAAAUCGAGAAAAAGUGGGUUUUGGUAGGGAAAGGAUGCGGUCAACGAUCUGACCUACACGGACUUUCUCCUUAUGGGGCUGUUAAAUGAGUUCAGCUUGAUUUUU
...((((((((((...............(((((....((((.((.....))))))..)))))..((((((.((((....)))).........))))))..)))))))))) ( -29.20)
>consensus
AGGAAAAAUCGAGGA_AAGUGGGUUUCGCUAGGGAAAGGGUGCGGUCAACGCUCUGACCUGCUCGGACUUUCUCCUUAUGGGGCUGUAACAUGAGUUGAGCUUGAUUUUU
...((((((((((....((..(((((.((((((...((((((.......))))))..)))))).)))))..)).((((((.........)))))).....)))))))))) (-28.18 = -28.78 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:57 2006