Locus 6217

Sequence ID	2R_DroMel_CAF1
Location	19,553,469 – 19,553,599
Length	130
Max. P	0.968506

overview

Window 7

Location	19,553,469 – 19,553,566
Length	97
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	90.19
Mean single sequence MFE	-27.34
Consensus MFE	-20.94
Energy contribution	-23.34
Covariance contribution	2.40
Combinations/Pair	1.00
Mean z-score	-2.58
Structure conservation index	0.77
SVM decision value	1.63
SVM RNA-class probability	0.968506
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19553469 97 + 20766785
AAUCAAAAUCGUCCCACAUGCAAACAGUCGUCUGCUGCACACACACAGCUAAACAU--------CAUGUGUAUGUAUGUAUGAACAUCCGCAAGGCGGCAAGGAA
...........(((....((....))(((((((((((........)))).......--------..((((.((((........)))).)))))))))))..))). ( -21.20)
>DroSec_CAF1 608 101 + 1
AAUCAAAAUCGUCCCACAUGC----AGCCGUCUGCUGCACACACACAGCCAGACAUAAUACGUACAUGUGUAUGUAUGUAUGUACAUCCGCAAGGCGGCAAGGAA
...........(((....(((----(((.....))))))........(((..(((((((((((((....)))))))).)))))....((....)).)))..))). ( -32.10)
>DroSim_CAF1 477 105 + 1
AAUCAAAAUCGUCCCACAUGCAAACAGCCGUCUGCUGCACACACACAGCCAGACAAAAUACGUACAUGUGUAUGUAUGUAUGUACAUCCGCAAGGCGGCAAGGAA
...........(((.((((((........((((((((........))).)))))...((((((((....))))))))))))))....((((...))))...))). ( -30.70)
>DroEre_CAF1 655 105 + 1
AAUCAAAAUCGUCACACAUGCAUACAGCCGUCUGCUGCACACACACAUCCAGACAUCAUACGUACAUGUGUAUGUAUGUAUGUACAUCCGCAAGGCGGCAAGGAA
..........(((..(((((((((((...(((((.((........))..)))))...(((((....))))).)))))))))))....((....)).)))...... ( -27.90)
>DroYak_CAF1 487 104 + 1
AAUCAAAAUCGUCACACAUGCAAACAGCCGUCUGCUG-ACACACACAACCAGACAUCACACGUACUUAUGUAUGUAUGUAUGUACAUCCGCAAGGCGGCAAGGAA
..........(((..(((((((.......(((((.((-.......))..))))).....((((((....)))))).)))))))....((....)).)))...... ( -24.80)
>consensus
AAUCAAAAUCGUCCCACAUGCAAACAGCCGUCUGCUGCACACACACAGCCAGACAUAAUACGUACAUGUGUAUGUAUGUAUGUACAUCCGCAAGGCGGCAAGGAA
..........(((..((((((........((((((((........)))).))))...((((((((....))))))))))))))....((....)).)))...... (-20.94 = -23.34 +   2.40)

alignment

secondary structure

dotplot

Window 8

Location	19,553,469 – 19,553,566
Length	97
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	90.19
Mean single sequence MFE	-31.52
Consensus MFE	-23.12
Energy contribution	-24.08
Covariance contribution	0.96
Combinations/Pair	1.11
Mean z-score	-1.60
Structure conservation index	0.73
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19553469 97 - 20766785
UUCCUUGCCGCCUUGCGGAUGUUCAUACAUACAUACACAUG--------AUGUUUAGCUGUGUGUGUGCAGCAGACGACUGUUUGCAUGUGGGACGAUUUUGAUU
.......((((...)))).(((((.((((((((((((((.(--------........))))))))))...((((((....))))))))))))))))......... ( -29.00)
>DroSec_CAF1 608 101 - 1
UUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUUAUGUCUGGCUGUGUGUGUGCAGCAGACGGCU----GCAUGUGGGACGAUUUUGAUU
((((.(((.(((...((((((((.((((.(((((....))))).))))))))))))(((((......)))))....))).----)))...))))........... ( -33.10)
>DroSim_CAF1 477 105 - 1
UUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUUUUGUCUGGCUGUGUGUGUGCAGCAGACGGCUGUUUGCAUGUGGGACGAUUUUGAUU
.(((...((((...))))(((((......))))).((((((((..((..(((((((.((((......))))))))))).))..)))))))))))........... ( -32.30)
>DroEre_CAF1 655 105 - 1
UUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUGAUGUCUGGAUGUGUGUGUGCAGCAGACGGCUGUAUGCAUGUGUGACGAUUUUGAUU
....(((.(((....(((((((.(((((.(((((....))))).))))))))))))...(..((((((((((.....))))))))))..)))).)))........ ( -33.20)
>DroYak_CAF1 487 104 - 1
UUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACAUAAGUACGUGUGAUGUCUGGUUGUGUGUGU-CAGCAGACGGCUGUUUGCAUGUGUGACGAUUUUGAUU
.......((((...)))).(((.(((((((((((((((((.((.(........))).))))))))))-..((((((....))))))))))))))))......... ( -30.00)
>consensus
UUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUGAUGUCUGGCUGUGUGUGUGCAGCAGACGGCUGUUUGCAUGUGGGACGAUUUUGAUU
.......((((...))))(((((......))))).((((((((.......(((((.(((((......))))))))))......)))))))).............. (-23.12 = -24.08 +   0.96)

alignment

secondary structure

dotplot

Window 9

Location	19,553,504 – 19,553,599
Length	95
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	86.88
Mean single sequence MFE	-30.20
Consensus MFE	-22.10
Energy contribution	-24.10
Covariance contribution	2.00
Combinations/Pair	1.12
Mean z-score	-2.30
Structure conservation index	0.73
SVM decision value	1.01
SVM RNA-class probability	0.900071
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19553504 95 - 20766785
AUCUGCAGGCAUACAUAUUUAAGGUGUGAUCGUUUCCUUGCCGCCUUGCGGAUGUUCAUACAUACAUACACAUG--------AUGUUUAGCUGUGUGUGUGCA
((((((((((...(((((.....)))))...((......)).))).))))))).........((((((((((.(--------........))))))))))).. ( -27.20)
>DroSec_CAF1 639 103 - 1
AUCUGCAGGCAUACAUAUUUUAGGUGUGAUCGUUUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUUAUGUCUGGCUGUGUGUGUGCA
((((((((((...(((((.....)))))...((......)).))).)))))))(((((((((((..((.(((((.......))))).))..))))))))))). ( -33.90)
>DroSim_CAF1 512 102 - 1
-UCUGCAGGCAUACAUAUUUAAGGUGUGAUCGUUUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUUUUGUCUGGCUGUGUGUGUGCA
-...(((.(((((((.......((((.((.....))..))))(((..(((((.((((.(((((........))))).)))))))))..)))))))))).))). ( -32.70)
>DroEre_CAF1 690 91 - 1
------------AUAUAUUUAAGGUGUGAUCGUUUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUGAUGUCUGGAUGUGUGUGUGCA
------------.......(((((...........)))))((((...)))).((((((((((((((.(((((((....)))).))).))..)))))))))))) ( -24.70)
>DroYak_CAF1 522 102 - 1
AUCCGCAGGCAUACAUAUUUAAGGUGUGAUCGUUUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACAUAAGUACGUGUGAUGUCUGGUUGUGUGUGU-CA
.......((((((((((..(((((((..(........)..).))))))(((((((.(((((.(((........))).))))))))))))..)))))))))-). ( -32.50)
>consensus
AUCUGCAGGCAUACAUAUUUAAGGUGUGAUCGUUUCCUUGCCGCCUUGCGGAUGUACAUACAUACAUACACAUGUACGUAUGAUGUCUGGCUGUGUGUGUGCA
.(((((((((...(((((.....)))))...((......)).))).))))))((((((((((((..((.((((.........)))).))..)))))))))))) (-22.10 = -24.10 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:51 2006