Locus 8085

Sequence ID	3L_DroMel_CAF1
Location	21,272,902 – 21,273,022
Length	120
Max. P	0.963257

overview

Window 2

Location	21,272,902 – 21,273,022
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-45.92
Consensus MFE	-41.72
Energy contribution	-42.41
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.91
SVM decision value	1.55
SVM RNA-class probability	0.963257
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21272902 120 + 23771897
CUAGACGUGUGGCCGCAACAAGGUCGCUGAUCUGUGAGAAAUUCGAUAUAGUCUCGACAUUGAGAAGCAUGUGAUCAGCGGCCGCAGACGAGGCUGCUCCGGCUACCACAUCAGCUCCCA
...((.(((((((((......(((((((((((((((.(.....).......(((((....)))))..)))).)))))))))))((((......))))..)))))).))).))........ ( -44.40)
>DroSec_CAF1 31202 120 + 1
CUAGACGUGUGGCCGCAACCAGGUCGCUGAUCUGUGAGAAAUUCGAUAUAGUCUCGACAUUGAGAAGCAUGUCAUCAACGGCCGCAGCCGAGGCUGCUCCGGCUGCCACAUCCGCUCCCA
..((..(((((((.((.....(((((.((((....((....)).(((((..(((((....)))))...))))))))).)))))(((((....)))))....)).)))))))...)).... ( -42.70)
>DroSim_CAF1 33463 120 + 1
CUAGACGUGUGGCCGCAACCAGGUCGCUGAUCUGUGAGAAAUUCGAUAUAGUCUCGACAUUGAGAAGCAUGUCAUCAGCGGCCGCAGCCGAGGCUGCUCCGGCUGCCACAUCCGCUCCCA
..((..(((((((.((.....((((((((((....((....)).(((((..(((((....)))))...)))))))))))))))(((((....)))))....)).)))))))...)).... ( -49.30)
>DroEre_CAF1 32366 113 + 1
CCAGCCUUGUGGCCGCAACUAGGUCGCUGAUCUGUGAGAAAUUGGAUAUAGUCUCGACAUUGAGAAGCAUGUGAUCGGCGGCCGCAGCAGAGGCUGCUCCGGCUGCCACAGCC-------
...((..((((((.((.....(((((((((((...((....))..((((..(((((....)))))...)))))))))))))))(((((....)))))....)).)))))))).------- ( -47.30)
>consensus
CUAGACGUGUGGCCGCAACCAGGUCGCUGAUCUGUGAGAAAUUCGAUAUAGUCUCGACAUUGAGAAGCAUGUCAUCAGCGGCCGCAGCCGAGGCUGCUCCGGCUGCCACAUCCGCUCCCA
......(((((((.((.....(((((((((((((((...............(((((....)))))..)))).)))))))))))(((((....)))))....)).)))))))......... (-41.72 = -42.41 +   0.69)

alignment

secondary structure

dotplot

Window 3

Location	21,272,902 – 21,273,022
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.25
Mean single sequence MFE	-46.45
Consensus MFE	-40.38
Energy contribution	-41.50
Covariance contribution	1.12
Combinations/Pair	1.11
Mean z-score	-1.79
Structure conservation index	0.87
SVM decision value	0.82
SVM RNA-class probability	0.859191
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21272902 120 - 23771897
UGGGAGCUGAUGUGGUAGCCGGAGCAGCCUCGUCUGCGGCCGCUGAUCACAUGCUUCUCAAUGUCGAGACUAUAUCGAAUUUCUCACAGAUCAGCGACCUUGUUGCGGCCACACGUCUAG
........((((((...((((.(((((((........)))((((((((((((........)))).((((............))))...))))))))....)))).))))..))))))... ( -42.30)
>DroSec_CAF1 31202 120 - 1
UGGGAGCGGAUGUGGCAGCCGGAGCAGCCUCGGCUGCGGCCGUUGAUGACAUGCUUCUCAAUGUCGAGACUAUAUCGAAUUUCUCACAGAUCAGCGACCUGGUUGCGGCCACACGUCUAG
.......(((((((((((((((.......))))))))((((((...((((((........)))))).(((((..(((....((.....))....)))..))))))))))).))))))).. ( -48.50)
>DroSim_CAF1 33463 120 - 1
UGGGAGCGGAUGUGGCAGCCGGAGCAGCCUCGGCUGCGGCCGCUGAUGACAUGCUUCUCAAUGUCGAGACUAUAUCGAAUUUCUCACAGAUCAGCGACCUGGUUGCGGCCACACGUCUAG
.......(((((((((((((((.......))))))))((((((...((((((........)))))).(((((..(((....((.....))....)))..))))))))))).))))))).. ( -50.80)
>DroEre_CAF1 32366 113 - 1
-------GGCUGUGGCAGCCGGAGCAGCCUCUGCUGCGGCCGCCGAUCACAUGCUUCUCAAUGUCGAGACUAUAUCCAAUUUCUCACAGAUCAGCGACCUAGUUGCGGCCACAAGGCUGG
-------(((((..((.((((.(((((...))))).))))(((.((((((((........)))).((((............))))...)))).))).....))..))))).......... ( -44.20)
>consensus
UGGGAGCGGAUGUGGCAGCCGGAGCAGCCUCGGCUGCGGCCGCUGAUCACAUGCUUCUCAAUGUCGAGACUAUAUCGAAUUUCUCACAGAUCAGCGACCUGGUUGCGGCCACACGUCUAG
.......(((((((((((((((.......))))))))((((((...((((((........)))))).(((((..(((....((.....))....)))..))))))))))).))))))).. (-40.38 = -41.50 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:51 2006