Locus 6435

Sequence ID	3L_DroMel_CAF1
Location	17,220,861 – 17,220,981
Length	120
Max. P	0.983858

overview

Window 0

Location	17,220,861 – 17,220,981
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.50
Mean single sequence MFE	-47.38
Consensus MFE	-45.20
Energy contribution	-45.36
Covariance contribution	0.16
Combinations/Pair	1.02
Mean z-score	-1.43
Structure conservation index	0.95
SVM decision value	0.84
SVM RNA-class probability	0.862798
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17220861 120 + 23771897
UUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUCGUAGUGGUGCAGGCAGUGGUCUUCGGCUGUGUGAGUAGUGGCACUGGCGAUAACCAAGCAACGAACCACAACCGCACCAAGGAGCGC
.(((((((((((.(.((....)).).)))))))....((((((.((..(((((..(((..(((.((.((.((.((....)).)).)))).))).))))))))..)))))))).))))... ( -48.60)
>DroSec_CAF1 104107 120 + 1
UUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUCGUAGUGGUGCAGGCAGUGGUCUUCGGCUGUGUGAGUAGUGGCGCUGGCGAUAACCAAGCAACGAACCACAACCGCACCAAGGAGCGC
.(((((((((((.(.((....)).).)))))))....((((((.((..(((((..(((..(((.((.((.((.((....)).)).)))).))).))))))))..)))))))).))))... ( -48.80)
>DroSim_CAF1 97837 120 + 1
UUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUCGUAGUGGUGCAGGCAGUGGUCUUCGGCUGUGUGAGUAGUGGCGCUGGCGAUAACCAAGCAACGAACCACAACCGCACCAAGGAGCGC
.(((((((((((.(.((....)).).)))))))....((((((.((..(((((..(((..(((.((.((.((.((....)).)).)))).))).))))))))..)))))))).))))... ( -48.80)
>DroEre_CAF1 107437 120 + 1
UUUCUGAGUGCAUCUGCAGUUGCCGCUGCACUCGUAGUGGUUCAGGCAGUGGUCUUCGGCUGUGUGAGUAGUGGCGCUGGCGAUAACCAAGCAACGAACCACAACCGCACCAAGGAGCGC
.....(((((((.(.((....)).).)))))))((.(((((((..((..((((..(((.(.((((.(....).)))).).)))..)))).))...))))))).))(((.(....).))). ( -46.90)
>DroYak_CAF1 110121 119 + 1
UUUCUGAGUGCAUCUGCAGUUGCCGCUGCACUCGUAGUGGUGCA-GCAGUGGUCUUCGGCUGUGUGAGUAGUGGCGCUGGCGAUAACCAAGCAACGAACCACAACCGCACCAAGGAGCGC
((((((((((((.(.((....)).).)))))))....((((((.-(..(((((..(((..(((.((.((.((.((....)).)).)))).))).))))))))..).)))))))))))... ( -43.80)
>consensus
UUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUCGUAGUGGUGCAGGCAGUGGUCUUCGGCUGUGUGAGUAGUGGCGCUGGCGAUAACCAAGCAACGAACCACAACCGCACCAAGGAGCGC
.(((((((((((.(.((....)).).)))))))....((((((.((..(((((..(((..(((.((.((.((.((....)).)).)))).))).))))))))..)))))))).))))... (-45.20 = -45.36 +   0.16)

alignment

secondary structure

dotplot

Window 1

Location	17,220,861 – 17,220,981
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.50
Mean single sequence MFE	-46.69
Consensus MFE	-42.24
Energy contribution	-43.04
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.90
SVM decision value	1.96
SVM RNA-class probability	0.983858
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17220861 120 - 23771897
GCGCUCCUUGGUGCGGUUGUGGUUCGUUGCUUGGUUAUCGCCAGUGCCACUACUCACACAGCCGAAGACCACUGCCUGCACCACUACGAGUGCAGCGGCAACUGCAGAUGCACUCGGAAA
....(((.(((((((((.((((((..(.(((((((....))))(((........)))..))).)..)))))).))).))))))....(((((((...((....))...)))))))))).. ( -48.70)
>DroSec_CAF1 104107 120 - 1
GCGCUCCUUGGUGCGGUUGUGGUUCGUUGCUUGGUUAUCGCCAGCGCCACUACUCACACAGCCGAAGACCACUGCCUGCACCACUACGAGUGCAGCGGCAACUGCAGAUGCACUCGGAAA
....(((.(((((((((.((((((.((.(((((((....))))).)).))...((........)).)))))).))).))))))....(((((((...((....))...)))))))))).. ( -47.40)
>DroSim_CAF1 97837 120 - 1
GCGCUCCUUGGUGCGGUUGUGGUUCGUUGCUUGGUUAUCGCCAGCGCCACUACUCACACAGCCGAAGACCACUGCCUGCACCACUACGAGUGCAGCGGCAACUGCAGAUGCACUCGGAAA
....(((.(((((((((.((((((.((.(((((((....))))).)).))...((........)).)))))).))).))))))....(((((((...((....))...)))))))))).. ( -47.40)
>DroEre_CAF1 107437 120 - 1
GCGCUCCUUGGUGCGGUUGUGGUUCGUUGCUUGGUUAUCGCCAGCGCCACUACUCACACAGCCGAAGACCACUGCCUGAACCACUACGAGUGCAGCGGCAACUGCAGAUGCACUCAGAAA
(((((....))))).((.((((((((..((.(((((.(((...((...............))))).)))))..)).)))))))).))(((((((...((....))...)))))))..... ( -43.96)
>DroYak_CAF1 110121 119 - 1
GCGCUCCUUGGUGCGGUUGUGGUUCGUUGCUUGGUUAUCGCCAGCGCCACUACUCACACAGCCGAAGACCACUGC-UGCACCACUACGAGUGCAGCGGCAACUGCAGAUGCACUCAGAAA
........(((((((((.((((((.((.(((((((....))))).)).))...((........)).)))))).))-)))))))....(((((((...((....))...)))))))..... ( -46.00)
>consensus
GCGCUCCUUGGUGCGGUUGUGGUUCGUUGCUUGGUUAUCGCCAGCGCCACUACUCACACAGCCGAAGACCACUGCCUGCACCACUACGAGUGCAGCGGCAACUGCAGAUGCACUCGGAAA
....(((.(((((((((.((((((.((.(((((((....))))).)).))...((........)).)))))).))).))))))....(((((((...((....))...)))))))))).. (-42.24 = -43.04 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:37 2006