Locus 1376

Sequence ID	3L_DroMel_CAF1
Location	4,010,029 – 4,010,246
Length	217
Max. P	0.594691

overview

Window 1

Location	4,010,029 – 4,010,149
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.87
Mean single sequence MFE	-30.85
Consensus MFE	-29.01
Energy contribution	-29.79
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-1.47
Structure conservation index	0.94
SVM decision value	-0.05
SVM RNA-class probability	0.506551
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4010029 120 + 23771897
CUCACAUGUAUCUCGGCAGCUAAUCGAAAUGCAAUCUGACGGAUGCAUCCGAAUCCUUCGGUCUGCUGCUGCAGAGUGAACCCACUUUAUUCCAAUUCCCACAGAAGUGUCUCAUAAUUG
..........((((((((((..(((((((((((.((.....)))))))........))))))..))))))).)))((((...((((((...............))))))..))))..... ( -30.56)
>DroSec_CAF1 4747 119 + 1
CUCGCAUGUAUCUCAGCCGCUAAUCGAAAUGCAAUCUGACGGAUGCAUGCUAAUCCUUCGGUCAGCUGCUGCAGAGUGAACUCACUUU-UUCCAAUUCUCACAGAAGUGUCUCAUAAUUG
..........(((((((.(((.(((((((((((.((.....)))))))........)))))).))).)))).)))((((...((((((-(............)))))))..))))..... ( -28.90)
>DroSim_CAF1 4774 119 + 1
CUCGCAUGUAUCUCAGCAGCUAAUCGAACUGCAAUCUGACGGAUGCAUCCGAAUCCUUCGGUCAGCUGCUGCAGAGUGAACUCACUUU-UUGCAAUUCCCACAGAAGUGUCUCAUAAUUG
..........(((((((((((.(((((((........).((((....)))).....)))))).)))))))).)))((((...((((((-(((.......)).)))))))..))))..... ( -33.10)
>consensus
CUCGCAUGUAUCUCAGCAGCUAAUCGAAAUGCAAUCUGACGGAUGCAUCCGAAUCCUUCGGUCAGCUGCUGCAGAGUGAACUCACUUU_UUCCAAUUCCCACAGAAGUGUCUCAUAAUUG
..........(((((((((((.(((((((((((.((.....)))))))........)))))).)))))))).)))((((...((((((...............))))))..))))..... (-29.01 = -29.79 +   0.78)

alignment

secondary structure

dotplot

Window 2

Location	4,010,149 – 4,010,246
Length	97
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	85.24
Mean single sequence MFE	-33.62
Consensus MFE	-24.29
Energy contribution	-25.35
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-1.54
Structure conservation index	0.72
SVM decision value	0.12
SVM RNA-class probability	0.594691
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4010149 97 - 23771897
CUUGUCAUGGGUGGAGUUGAGCCCUUCACAAUG-----------------GUGCCCGUCUGAAGUGCCACUAAUUAGGGGCUUUGGACCUAAGCUAGUACCAGGAUGUAAACAA
...(((.(((((((((.......))))))..((-----------------((....(((..((((.((........)).))))..)))....))))...))).)))........ ( -29.80)
>DroSec_CAF1 4866 96 - 1
CUUGUCAUGGGCGGAGUUGAGUCGUCCACAAUG-----------------GUGUCCGUCCGAAGUGCCACUAAUUAGGGGCUUUGGAC-UGAGCUAGUCCCAGGAUGUAAACAA
...(((.(((((..((((.((.((..(((....-----------------)))..))((((((((.((........)).)))))))))-).)))).).)))).)))........ ( -32.90)
>DroSim_CAF1 4893 96 - 1
CUUGUCAUGGGUGGAGUUGAGUCCUCCACAAUG-----------------GUGUCCGUCCGAAGUGCCACUAAUUAGGGGCUUUGGAC-UGAGCUAGUCCCAGGAUGUAAACAA
...(((.(((((((((.......))))))..((-----------------((.((.(((((((((.((........)).)))))))))-.))))))...))).)))........ ( -35.70)
>DroYak_CAF1 5613 113 - 1
UUUGUCAGGGGCGGAGUUGAGCCCUCCACAAUGGAUUUGGUUGUACUAGGGUGUCCGUCUGAAGUGCCACUAAUUAGGGGCUUUGGAC-UGAGCUAGUCCGAGUAUGUAAACAA
.((((..(((((........)))))..))))((((((.((((......((....))(((..((((.((........)).))))..)))-..))))))))))............. ( -36.10)
>consensus
CUUGUCAUGGGCGGAGUUGAGCCCUCCACAAUG_________________GUGUCCGUCCGAAGUGCCACUAAUUAGGGGCUUUGGAC_UGAGCUAGUCCCAGGAUGUAAACAA
...(((.(((((((((.......)))))).....................((....(((((((((.((........)).)))))))))....)).....))).)))........ (-24.29 = -25.35 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:59 2006